This document provides an overview of COVID-19 and summarizes key information about the virus. It discusses that COVID-19 is caused by a novel coronavirus called SARS-CoV-2. The document covers epidemiology of the virus, symptoms, at-risk groups, testing guidelines, treatment approaches which are currently symptomatic, and prevention methods like hand washing and social distancing. It also summarizes guidance on specimen collection, laboratory testing, and current investigational drugs and vaccines being explored to tackle the pandemic.

1. COVID-19
This course provides a general introduction and awareness to
COVID-19 and is intended for public health professionals and
medical and paramedical students in developing countries.
Dr.Deepa Babin
Associate professor, Microbiology,SRMCRC,TVM

3. Coronaviruses
• Large family of viruses that are known to cause
illness ranging from the common cold to more
severe diseases such as Severe Acute
Respiratory Syndrome (SARS-China 2003)and
Middle East Respiratory Syndrome (MERS –Saudi
Arabia 2012)
Middle East Respiratory Syndrome (MERS –Saudi
Arabia 2012)
• A novel coronavirus (COVID-19) was identified in
2019 in Wuhan, China with an outbreak of
respiratory illness
• A new coronavirus that has not been previously
identified in humans

4. What are Corona viruses?
• Cause of significant
percentage of all common
colds in human adults.
• Ccolds in humans primarily in
the winter and early springthe winter and early spring
season.
• Primarily infect the upper
respiratory and
gastrointestinal tract of
mammals and birds.

5. Classification
• Coronaviruses (CoVs) (order Nidovirales,
family Coronaviridae, subfamily Coronavirinae)
are enveloped viruses with a positive sense,
single-stranded RNA genome.
• With genome sizes ranging from 26 to 32• With genome sizes ranging from 26 to 32
kilobases (kb) in length, CoVs have the largest
genomes for RNA viruses.
• Based on genetic and antigenic criteria, CoVs
have been organised into three groups: α-CoVs,
β-CoVs, and γ-CoVs

6. Coronaviral genome
• Coronaviral genome encodes four major structural
proteins: the spike (S) protein, nucleocapsid (N)
protein, membrane (M) protein, and the envelope (E)
protein, all of which are required to produce a
structurally complete viral particlestructurally complete viral particle
• HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-
HKU1, are mild and self-limiting, SARS-CoV and MERS-
CoV cause severe infections that lead to high
mortality rates
• And the latest COVID-19 cause pandemic associated
severe respiratory conditions

7. Morphology

8. COVID 19 STRUCTURE
• The CoV envelope (E) protein
is a small, integral membrane
protein involved in several
aspects of the virus’ life cycle,
such as assembly, budding,
envelope formation, and
pathogenesis.
• Name derived from the
Latin corona, meaning crown.
• Viral envelope under electron
microscopy appears crown-like
due to small bulbar
projections formed by the viral
spike (S) peplomers.

9. Naming of New Virus
• Disease -coronavirus disease- (COVID-
19)
• Virus-
Severe acute respiratory syndrome
coronavirus 2
(SARS-CoV-2)(SARS-CoV-2)
• Origin is uncertain although bats and
pangolins currently implicated.
– The preliminary genetic analysis appears
to find a great similarity to bat SARS-like
coronavirus (genus Betacoronavirus,
subgenus Sarbecovirus.
• Appears to be spread more easily
than SARS or MERS

10. Epidemiology
• Most commonly occurring in winter and
early spring.
– Incubation period -Mean of 6 days, range
2-12.
– For people quarantined, 14d observation
recommended to exclude infection,
though 24d asymptomatic time from
exposure described.exposure described.
– Viral shedding occurs following recovery,
but unclear what role this plays in
transmission.
– Children and intrafamilial spread appear
to be a growing means of transmission..
• Shedding may occur longer or also
occur in asymptomatic individuals.

11. Symptoms
– Fever (83-98%)
– Cough (46-82%, usually
dry)
– Shortness of breath at
onset (31%)
– Myalgia or fatigue (11-
44%)
– Less common– Less common
symptoms:
• Pharyngitis
• Headache
• Productive cough
• GI symptoms
– Have been described as a
presenting symptom
• Hemoptysis

12. Emergency warning signs
• If you develop emergency warning signs for COVID-19 get
medical attention immediately.
• Emergency warning signs include*:
• Trouble breathing
• Persistent pain or pressure in the chest
• New confusion or inability to arouse• New confusion or inability to arouse
• Bluish lips or face
• Fever may not be present in some patients, such as those
who are very young, elderly, immunosuppressed, or
taking certain medications.
• Clinical judgement should be used to guide testing of
patients in such situations.

13. Who are at risk?
• Children, Older adults,
Pregnancy and people
who have severe
underlying medical
conditions like heart or
lung disease or diabetes
conditions like heart or
lung disease or diabetes
seem to be at higher risk
for developing more
serious complications
from COVID-19 illness.

14. Who should be tested?
• Not everyone needs to be tested for COVID-
19.
• Most people have mild illness and are able to
recover at home or even asymptomatic
• There is no treatment specifically approved
for this virus.
• Testing results may be helpful to inform
decision-making about who you come indecision-making about who you come in
contact with.
• Decisions about testing are at the discretion
of state and local health departments and/or
individual clinicians.
• Clinicians should work with their state and
local health departments to coordinate
testing through public health laboratories, or
work with clinical laboratories.

17. •Confirmed cases•Confirmed cases •Confirmed
deaths
•Confirmed
deaths
• Countries,
areas or
• Countries,
areas or
TODAY 31 March 2020, 03:17 GMT+5:30
Coronavirus disease (COVID-19)
697,244
deathsdeaths
33,257
areas or
territories
areas or
territories
204

20. RIGHT WAY

27. Where should nasopharyngeal swabs be performed
on a known or suspected COVID-19 patient, and with
what PPE?
• The collection of nasopharyngeal (NP) swabs
from patients with known or suspected COVID-
19 can be performed in a regular examination
room with the door closed.
• Use of an airborne infection isolation room for
nasopharyngeal specimen collection is not
required.required.
• Health care provider(HCP) in the room should
wear an N95 or higher-level respirator (or
facemask if a respirator is not available), eye
protection, gloves, and a gown.
• If respirators are not readily available, they
should be prioritized for other procedures at
higher risk for producing infectious aerosols
(e.g., intubation), instead of for collecting NP
swabs.

28. Specimen Type and Priority•
Nasopharyngeal specimen is the
preferred choice for swab-based
SARS-CoV-2 testing.
The following are acceptable
alternatives:
An oropharyngeal (OP) specimen,
A nasal mid-turbinate (NMT) swab
An anterior nares specimen
For patients who develop a
productive cough, sputum
When it is clinically indicated (e.g.,
those receiving invasive
mechanical ventilation), a lower
Maintain proper infection
control when collectingproductive cough, sputum
should be collected and tested
for SARS-CoV-2. The induction
of sputum is not
recommended.
mechanical ventilation), a lower
respiratory tract aspirate or
bronchoalveolar lavage sample
should be collected and tested as a
lower respiratory tract specimen.
control when collecting
specimens.
Biosafety for handling and
processing specimens from
suspected case patients.
For NS, a single
both nares.
For NS, a single
polyester swab with a
plastic shaft should
be used to sample
both nares.
NS or NMT swabs should be
placed in a transport tube
containing either viral
transport medium, Amies
transport medium, or sterile
saline.
If both NP and OP
swabs both are
collected, they should
be combined in a single
tube to maximize test
sensitivity

29. Upper respiratory tract
Nasopharyngeal swab (NP) /oropharyngeal swab
(OP)
• Use only synthetic fiber swabs with plastic shafts.
• Do not use calcium alginate swabs or swabs with wooden shafts, as they
may contain substances that inactivate some viruses and inhibit PCR
testing.
• Place swabs immediately into sterile tubes containing 2-3 ml of viral
transport media.
• If both swabs are used, NP and OP specimens should be combined at
collection into a single vial. OP swabs remain an acceptable specimen
type.
collection into a single vial. OP swabs remain an acceptable specimen
type.
• Nasopharyngeal swab: Insert a swab into nostril parallel to the palate.
• Swab should reach depth equal to distance from nostrils to outer
opening of the ear. Leave swab in place for several seconds to absorb
secretions. Slowly remove swab while rotating it.
Oropharyngeal swab (e.g., throat swab): Swab the posterior pharynx,
avoiding the tongue.
• Nasopharyngeal wash/aspirate or nasal aspirate
• Collect 2-3 mL into a sterile, leak-proof, screw-cap sputum collection cup
or sterile dry container.

30. Storage
• Store specimens at 2-8°C for up to 72 hours
after collection.
• If a delay in testing or shipping is expected,
store specimens at -70°C or below.store specimens at -70°C or below.

31. Laboratory testing
• CDC 2019-nCoV Real-Time RT-PCR
Diagnostic Panel contains the
following:
• 2019-nCoV_N1, 2019-nCoV_N2 and
2019-nCoV_N3 primers and probes
that target the nucleocapsid (N)
gene and are designed for both
universal detection of SARS-like
coronavirus as well as specific
universal detection of SARS-like
coronavirus as well as specific
detection of the 2019-nCoV;
• RP primers and probes that target
the Human RNase P gene
• nCoVPC, the 2019-nCoV positive
control used in the assay.

32. Laboratory Mannual
Use either a certified
Class II Biological Safety
Cabinet (BSC) or
additional precautions
to provide a barrier
between the specimen
and personnel.
Personal protective
equipment (PPE), such as a
surgical mask or face shield,
or other physical barriers,
like a splash shield
centrifuge safety cups; and
sealed centrifuge rotors to
reduce the risk of exposure
to laboratory personnel.
Decontaminate work surfaces and
equipment with appropriate disinfectants.
Use disinfectants with label claims to be
effective against SARS-CoV-2external icon.
Follow manufacturer’s recommendations for
use, such as dilution, contact time, and safe
handling.
Laboratory Waste Management
Handle laboratory waste from
testing suspected or confirmed
COVID-19 patient specimens as all
other biohazardous waste in the
laboratory.
Currently, there is no evidence to
suggest that this laboratory waste
needs any additional packaging or
disinfection procedures
Specimen Packing and Shipping
Pack and ship suspected and
confirmed SARS-CoV-2 patient
specimens, cultures, or isolates
as Biological Substance,
Category B,
Personnel must be trained to
pack and ship according to the
regulations and in a manner
that corresponds to their
function-specific
responsibilities.

33. Treatment
• There is no specific antiviral treatment
recommended for COVID-19, and no vaccine is
currently available.
• The treatment is symptomatic, and oxygen
therapy represents the major treatmenttherapy represents the major treatment
intervention for patients with severe infection.
• Mechanical ventilation may be necessary in
cases of respiratory failure refractory to oxygen
therapy, whereas hemodynamic support is
essential for managing septic shock.

34. PREVENTION
• The best way to prevent illness is to
avoid being exposed to this virus.
• The virus is thought to spread
mainly from person-to-person.
• Between people who are in close
contact with one another (within
about 6 feet).about 6 feet).
• 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.

35. PREVENTION
• Clean your hands often
• Wash your hands often with soap and
water for at least 20 seconds especially
after you have been in a public place, or
after blowing your nose, coughing, or
sneezing.
• If soap and water are not readily• If soap and water are not readily
available, use a hand sanitizer that
contains at least 60% alcohol.
• Cover all surfaces of your hands and rub
them together until they feel dry.
• Avoid touching your eyes, nose, and
mouth with unwashed hands.
• Fumigation using sodium hypochloride

37. Drugs currently under investigation
• Remdesivir (Gilead; used to treat Ebola)
– Currently under study in a trial in Wuhan and U.S.; activity is seen in
vitro with SARS-2-CoV, MERS-CoV (also including MERS-CoV primate
studies)
– Likely the most promising drug
– Drug has been used in the U.S. under compassionate use; however,
unclear how long this will last
• Chloroquine (or hydroxychloroquine; HCQ) has been reported• Chloroquine (or hydroxychloroquine; HCQ) has been reported
to have some efficacy in vivo and in limited, very low-quality
evidence for COVID-19 pneumonia, the mechanism may be by
interfering with cellular acidification in the phagolysosome.
• ASC09/oseltamivir, ritonavir/oseltamivir, oseltamivir
• Azvudine
• All under trial with limited possibilities ..............

38. VACCINES UNDER TRIAL

39. Take everyday preventive steps
• Wash your hands frequently
• Avoid touching your eyes, nose, and mouth.
• Stay home when you are sick.
• Cover your cough or sneeze with a tissue, then• Cover your cough or sneeze with a tissue, then
throw the tissue in the trash.
• Clean and disinfect frequently touched objects
and surfaces
• Social Distancing

41. Resources
• WHO has provided recommendations to reduce risk of
transmission from animals to humans
• WHO has published an updated advice for international traffic
in relation to the outbreak of the novel coronavirus 2019-nCoV.
• WHO has activated the R&D blueprint to accelerate
diagnostics, vaccines, and therapeutics.diagnostics, vaccines, and therapeutics.
• OpenWHO is an interactive, web-based, knowledge-transfer
platform offering online courses to improve the response to
health emergencies.
• COVID-19 courses can be found here and courses in additional
national languages here.
• CDC Laboratory Biosafety Frequently Asked Questions
• EPA List N: Disinfectants for Use Against SARS-CoV-2external
icon
• Saf-T-Pak Packaging Checklist, see Category Bpdf icon