Manoj Mahato

1. CLINICAL MICROBIOLOGIST MR. MANOJ MEHTA
Coronavirus

2. The source of the virus is not yet known
It is known:
-to have originated from an animal source, likely a bat
-the first reported infections in China were linked to a live animal market
-the virus is now spreading from person to person.
It appears to have first emerged in Wuhan, China, in late 2019.
The outbreak has since spread across China to other countries around the world. By the
end of January, the new coronavirus had been declared a public health emergency of
international concern by the WHO
Origins of Coronavirus

3. 14/04/2024
1. Transmission
between host
animals
2. Transmission from the
host animal to humans
3. Human-to-human
transmission
Origins of Coronavirus

4. Coronaviruses belong to the Coronaviridae family in the Nidovirales order
Corona represents crown-like spikes on the outer surface of the virus; thus, it was named
as a coronavirus
Coronaviruses cause illness in humans, and others cause illness in animals, such as bats,
camels, and civets
Severe acute respiratory syndrome (SARS) is a viral respiratory illness caused by a
coronavirus, called SARS-associated coronavirus (SARS-CoV)
The disease mainly affects the “respiratory system” – the lungs and airways that allow us
to breath
Previous Coronaviruses have included SARS- CoV and MERS-CoV
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new strain of
coronavirus that has not been previously identified
CORONAVIRUS

5. Medium-sized virus size, but largest
mRNA genome
Enveloped +ve stranded RNA
mRNA encased in nucleocapsid
Lipid Bilayer – Soap works to disrupt
this!
Corona = Crowns for Spikes
Glycoprotein Spike (S) Peptomer
Spikes allow it to attach to human cell
receptors in upper or lower airway
CORONAVIRUS

6. COVID-19 is the infectious disease caused by the most recently discovered coronavirus
as SARS-CoV-2
It was reported for the first time in China in December 2019 and has now spread
throughout the world as a pandemic disease.
COVID-19 is a disease that affects the lungs
It is spread through droplets of saliva when an infected person coughs, sneezes or speaks
People can infect others from 2 days before they develop symptoms
Important symptoms are difficulty breathing, dry cough and fever
About 80% of infected people will have mild or moderate symptoms
About 20% of infected people will have severe symptoms and need hospital care
COVID-19 DISEASE

7. SNEEZE/ COUGH
BY INFECTED PERSON
INFECTED DROPLETS
GET ON YOUR HAND
AND WHEN TOUCH
ANY SURFACE OR PERSON
VIRUS
TRANSFERRED!!
07
SNEEZE/ COUGH
BY INFECTED PERSON INFECTED DROPLETS
INFECTED DROPLETS
GET ON YOUR HAND
VIRUS
TRANSFERRED!!
INFECTED DROPLETS
MODES OF TRANSMISSION

8. COVID-19 is spread from person to person
mainly through coughing, sneezing, and talking
and breathing
It is spread through droplets from the nose and
mouth- example by talking loud, singing,
shouting, coughing or sneezing.
 Droplets containing the virus can also fall onto
surfaces. If you touch that surface and then touch
your eyes, nose or mouth, you could also
become infected
Incubation 2-14 days (outlier 27 days)
Symptom onset median: Day 5-6 from
exposure
MODES OF TRANSMISSION

9. Chain of infection

10. Howdoes thevirus cause disease

11. Coronaviruses enter the human body by being inhaled or via direct touch to the mouth,
nose and eyes.
They bind to and infect the cells lining the upper and lower airways and lungs.
On average, symptoms will develop five days after infection, but this can range from
two to 12 days
Symptoms generally occur after the virus causes direct damage to the cells of the
airways and lung, or when the virus triggers an immune response.
 Irritation of the airway produces a sore throat and cough and sometimes a blocked or
runny nose.
A cough is a reflex to clear the airway of perceived phlegm, though COVID-19 usually
produces a dry cough.
Howdoes thevirus cause disease

12. As part of the immune response to infection, signalling molecules called cytokines are
produced. Cytokines help to mediate immunity through communication between cells,
but they can also have a number of adverse effects during the course of illness.
They contribute to fever and fatigue, muscle aches, headache and a loss of appetite.
 Diarrhoea, nausea and vomiting are rarer but may occur when the virus is present in
the gut. The duration of symptoms ranges from one to three weeks depending on the
severity of illness.
.About 80% of people with COVID-19 have mild disease and never require
hospitalisation. For those who do develop more serious illness, it is most frequently a
form of pneumonia.
Howdoes thevirus cause disease

13. The estimated incubation period is 3 to 6 days but can vary between 1 and 11 days.
Symptoms may vary by age but the main symptoms of coronavirus are:
• a new, continuous cough – coughing for more than an hour, or 3 or more coughing
episodes in 24 hours
• a high temperature
• a loss or change to sense of smell or taste
COVID-19 SYMPTOMS

14. Other symptoms reported include:
• fatigue and lethargy
• shortness of breath
• headache
• sore throat
• aching muscles
• diarrhoea and vomiting
COVID-19 SYMPTOMS

15. Symptoms may begin gradually and are usually mild.
The majority of people (around 80%) have asymptomatic to moderate disease and recover
without needing hospital treatment
Around 15% may get severe disease including pneumonia
Older people and those with underlying medical problems such as high blood pressure,
heart and lung problems, diabetes, or cancer are more likely to develop serious illness
Around 5% become critically unwell. This may include septic shock and/or multi-organ and
respiratory failure
The infection fatality rate (the proportion of deaths among all infected individuals) is
estimated to be 0.9% but it varies according to age and sex. It is lower in younger people
(0.5% for those 45-64 years) and higher in those over 75 years of age (11.6%)
COVID-19 SYMPTOMS PROGRESSION

16. Older people : risk of infection increases after 60 years old
People with
-Diseases that affect the lungs (e.g. TB and asthma) or heart,
-Diabetes, kidney or liver disease,
-Conditions that affect the immune system, such as cancer
People who are overweight
Men appear to be more vulnerable than women
Who has higher risk from COVID-19?

17. Complications from COVID-19 can be severe and fatal.
The risk of developing complications increases with age and is greater in those with underlying
health conditions. The type of complication that can develop may include:
• venous thromboembolism
• heart, liver and kidney problems
• neurological problems
• coagulation (blood clotting) failure
• respiratory failure
• multiple organ failure
• septic shock
Complications of Covid-19 disease

18. Laboratory diagnosis
Polymer Chain Reaction (PCR method)
COVID-19 Antigen Test
COVID-19 Antibody Test
Types of Covid 19 testing

19. RT
-PCR is a Molecular tests that are designed to detect an active infection with SARS-
CoV-2, the coronavirus that causes COVID-19.
Themost common types of tests usedto determine if youhave an active COVID-19 infection
It is a most accurate method of diagnosing COVID-19.
Known as “gold standard” Test
◦ Target combination of genes: Nucleocapsid (N),
◦ Open reading frame 1ab (Orf),
◦ Envelope (E), or the RNA dependent RNA polymerase (RdRp)
RT-PCR Test

20. Real-time Polymerase Chain Reaction of RNA
◦ Nasal AND Orophangeal Swabs (Collect 2 swabs)
◦ Sputum better (but more dangerous to collect?)
◦ Stool – not generally used for testing
◦ Blood or urine – virus not detected; blood could be tested for IgM, IgG later. DO get (bacterial)
blood cultures for any sick patient.
PCR ~ 60-80% sensitive
◦ A single negative RT-PCR doesn't exclude COVID-19 (especially if obtained from a
nasopharyngeal source or relatively early in the disease course).
◦ If RT-PCR is negative but suspicion remains, consider ongoing isolation and re-sampling several
days later.
◦ Sensitivity from private labs may vary; no data yet. Also dependent on collection technique and
timing – early test on asymptomatic may not be accurate
RT-PCR Test

21. Collect appropriate samples
Lower respiratory tract samples are preferred because the lower respiratory tract is the
primary site of infection
Take combined nasopharyngeal and oropharyngeal swabs in ambulatory patients and
sputum (if produced) and/or tracheal aspirate or bronchoalveolar lavage in patients with
more severe respiratory disease
Use universal/viral transport medium for swabs, if available; sterile container for
sputum and aspirates
Specimen collection for SARS-CoV-2 testing

22. Nasopharyngeal swab
Oropharyngeal swab
How to collect nasopharyngeal and oropharyngeal swabs

23. Sample
processing
(biosafety
cabinet)
Automated
nucleic acid
extraction
Real time -
reverse
transcription
PCR
Reporting
~1.5 hour ~3 hours ~2.5 hours
Timeline
Testing Work Flow of RT- PCR Test

24. S-Gene
E-Gene
Analysis of RT- PCR Test

25. Interpretation of Results
Target E
Gene
Target S
Gene
Internal
control
Results Interpretation Report
Detected Detected Detected Omicron and SARS-CoV-2 detected Positive
ND Detected Detected SARS-CoV-2 RNA detected Positive
ND ND Detected Only internal control detected Negative
ND ND ND RT-PCR inhibition or reagent failure Indeterminate
Detected ND Detected B-ßCov detected only Beta coronavirus
detected
o E (envelope) gene detects all members of the lineage B of the beta-CoVs which are all SARS, SARS-like and SARS-related viruses
o S (spike) gene specifically detects the SARS-CoV-2
o *An S-gene neg/E-gene pos would indicate positivity for SARS (including but not necessarily limited to SARS-CoV-2). This result does not rule
out SARS-Cov-2—

26. Those that detect the presence of pieces from the
actual SARS-CoV-2 known as antigen tests.
COVID-19 antigen tests require a sample of cells that
come from your upper respiratory tract.
In particular, they can be taken from inside your nose
or from your nasopharynx, which is the top part of the
throat that is behind the nose.
Thetest sample is taken using a cotton swab that is
inserted into your nostril.
Can diagnose an active infection with Covid
Sample: Nasal or throat swab
Covid 19 Antigen Test

27.  Thereare multiple types of tests for COVID-19. Testing for active
infection can be used for diagnosis, screening, or monitoring:
 -Diagnosis; is testing for COVID-19 in people who have shown
symptomsof the disease.
 -Screening; is testing in people who have not shownsymptoms. For
COVID-19,screening is often done for people who have been in close
contact with someone who has tested positive.
 -Monitoring; is a method of follow-up to determine if a person who
was previously diagnosed with COVID-19 continues to test positive
Rapid test with results in ~15 minutes
Covid 19 Antigen Test

28. Antibody tests can determine if youhaveantibodies against a
specific virus,such asSARSor COVID-19.
Theymayhelp diagnose an active infection, Thosethat detect
evidence of current or past infection in cells produced by the
patient’s immune systembut do not provide a definite diagnosis.
Antibody testing is done with a blood sample and isalso
known as serology testing.
 It can be performed in a laboratory or with on-site, point-
of-care testing.
Resultsare generally reported within 30 minutes at most
locations.
It is also used in research to better understand the COVID-19
pandemic.
Covid 19 Antibody tests

29. IgM Antibodies
Antibody Detection
IgG Antibodies
Molecular Detection
Viral RNA
Symptom
Onset
Infection
Week -1 Week 1 Week 2 Week 3 Week 4 Week 5 Week 6
Timing of Antibody Response to SARS-CoV-2
New virus = no pre-existing antibodies or immunity
Many develop Abs ~1-2 weeks after symptoms
Due to delay in seroconversion, Abs do not play
a routine role in diagnosis
>95% of patients are Ab positive after 2 weeks
Some patients may not seroconvert
 - Immunostatus
 - Assay dependent?
 - Severity of illness?
IgM declines 5-7 weeks post onset
IgG remains positive for ≥10 weeks post onset

30. Most Common:
◦ WBC usually normal, Lymphopenia in 80%, Mild thrombocytopenia
◦ Low Procal; Bacterial coinfection rare
◦ CRP and D-Dimer elevated proportionate to severity (marker of poor prognosis); DIC over time
◦ Increased ALT/AST to 70-100 range; Occasional increased alk phos
◦ Mild elevation of creatinine
◦ Generally normal troponin
CXR (sensitivity 59%):
◦ Bilateral patchy or reticular infiltrates, perihilar infiltrates occasionally
CT scan (sensitivity 86%; much better than RT-PCR!)
◦ Bilateral diffuse ground glass opacities, multifocal patchy consolidation, interstitial changes
◦ Changes prior to severe symptom onset!
ECHO:Normal EF prior to late-onset sudden cardiogenic shock with dropping to EF <10%
Other diagnostic Test

31. There is currently no specific treatment for COVID-19
For mild cases in home isolation, patients can be advised to:
drink plenty of liquids,
take paracetamol or ibuprofen for fever or pain
eat and rest as well as possible
If the person starts to find it difficult to breath, it is important to go immediately to the nearest
health facility
They should cover their mouth and nose with a medical or fabric mask.
In hospital, “supportive” care is given for moderate and severe cases. This can include IV fluids,
pain relief, oxygen or other breathing support
Treatment

32. Paracetamol is preferred for relief of pain or fever rather than nonsteroidal anti-inflammatory
drug (NSAID)
Cough suppressants, such as codeine-containing cough mixtures are not indicated
Opioids such as morphine should not be used and may only be used with due caution and careful
monitoring
ACEi (Angiotensin converting enzyme inhibitors) or ARBs (Angiotensin receptor blockers)
might upregulate ACE2 receptors, the binding site for SARS-CoV-2, within tissues including the
lung and heart, prompting theoretical concerns that this might place patients at risk of worse
outcomes with COVID-19. But there is no evidence hence discontinuation of these agents not
recommended.
Treatment

33. Lopinavir/Ritonavir (Kaletra – protease inhibitors)
Ribavirin
Remdesivir
Chloroquine/hydroxychloroquine
High dose IV Vitamin C
IVIG
Serum antibodies of recovered patients
Treatment

34. Antiviral
therapies
Immune
modulator
therapies
Healthy, no
infection
Not hospitalized, no limitations Not hospitalized, with limitations
Hospitalized, no
active medical
problems
Hospitalized, not on
oxygen
Hospitalized, on
oxygen
Hospitalized, high flow
oxygen/non invasive
ventilation
Hospitalized, mechanical
ventilation/ECMO
Exposed / Asymptomatic
Infected
Early Symptomatic Hospital Admission ICU Admission
No Illness
Remdesivir
Convalescent Plasma
Baricitinib +
remdesivir
Dexamethasone + remdesivir
Monoclonal Antibodies
• Bamlanivimab
• Bamlanivimab +
etesevimab
• Casirivimab +
imdevimab
EUA issued
FDA approved
Dexamethasone
Dexamethasone + tocilizumab
COVID-19 Therapy by Illness
Phase

35. Wash hands frequently with soap and water or use sanitizer
and always before moving to the next place
Cough and sneeze hygiene
Wear medical mask, eye protection, gloves & apron Avoiding
touching
Clean and disinfect surfaces and equipment
Physical distancing
Isolation when sick
Quarantine if contact
Protecting people at high risk
Alerting when someone has COVID19-like symptoms
Stay current on COVID-19 vaccinations
Prevention and Control

36. HIGH RISK
GROUP
SOCIAL
DISTANCING
RESPIRATORY
HYGIENE
HAND HYGIENE
Prevention and Control

37. Quarantine and Isolation
Quarantine is what contacts of a case are asked to do.
• It is a 14-day period
• Where contacts are asked not to leave their homes
• To monitor their symptoms
• And keep communication with their CHW contact tracer

38. Quarantine and Isolation
Home Isolation is what cases are asked to do if they have mild symptoms of COVID-19.
• It is a period of at least 7 days AND until the person no longer has symptoms
• People are asked not to leave their homes,
• To practice measures to reduce transmission
• And keep in communication with their CHW
.

39. Stay Home if Sick
Wash Your Hands Small, Stable Groups
Cleaning Face Masks
Vaccination
Healthy Air
Prevention and Control

40. A vaccine is a product designed to help prevent diseases.
Vaccines can help individuals from getting diseases such as:
 Chickenpox
 Influenza (flu)
 COVID-19
Vaccines keep communities safe and healthy by:
• Supporting herd immunity
• Preventing a disease from spreading
VACCINATION

41. Vaccination Development

42. None of the COVID-19 vaccines contain the whole or weakened viruses, like
influenza, chickenpox or MMR.
 They either use a messenger RNA (mRNA) and we call it an mRNA vaccine (Moderna
and Pfizer), or they contain a piece of the covid virus (J&J vaccine).
There is no possibility of getting the COVID virus with these types of vaccines
COVID-19 Vaccines

43.  A virus can be used to make a vaccine in different ways:
 Using a whole virus by using it when it is dead or weakened (like Chickenpox,
flu and MMR)
 Using a piece of the virus (like tetanus and hepatitis B vaccines are made)
 Without using any of the virus itself (how mRNA vaccines are made)
 For COVID, this type of vaccine is called an mRNA vaccine. This type of vaccine
does not contain any virus at all, and it does not create a virus in your body, so you
cannot get the infection from the vaccine
How Vaccines Are Made

44. HOW mRNA VACCINE WORK

45. mRNA vaccines are a new type of vaccine to protect against infectious diseases.
To trigger an immune response, many vaccines put a weakened or inactivated germ
into our bodies. Not mRNA vaccines.
Instead, they teach our cells how to make a protein or even just a piece of a protein that
triggers an immune response inside our bodies.
That immune response, which produces antibodies, is what protects us from getting
infected if the real virus enters our bodies.
HOW mRNA VACCINE WORK

46.  Use messenger RNA (mRNA)
 mRNA is a protein that:
 Gives a body instructions to recognize the COVID virus that causes the disease and to
kill it before it can make you sick
 mRNA is not DNA, and does not interact or change an individual’s DNA in any way
Pfizer and Moderna COVID-19 Vaccines

47. The J&J vaccine is not an mRNA vaccine. Instead, the J&J vaccine uses another virus,
called an adenovirus (a virus that causes the common cold).
The adenovirus is killed and then a fake spike protein is attached.
After someone gets the vaccine, their body prepares their antibody protectors against
the spike protein, like the mRNA vaccines.
 If the person catches the COVID, their antibody protectors recognize the spike protein
and attack and kill the covid before it can make them sick.
Johnson & Johnson COVID-19 Vaccine

48. AstraZeneca COVID-19 vaccine is a viral vector vaccine which uses a weakened adenovirus as
a carrier to deliver the SARS-CoV-2 antigen.
The adenovirus has been modified so that it cannot replicate (grow and multiply by making
copies of itself) in human cells and therefore cause any disease.
The genes that encode for the spike protein on the SARS-CoV-2 virus have been inserted into
the adenovirus's genetic code to make the vaccine.
When the vaccine is injected, it enters the host's cells which then manufacture the spike protein.
This then stimulates the immune system which reacts by producing antibodies and memory cells
to the SARS-CoV-2 virus without causing disease.
AstraZeneca COVID-19 vaccine

49. Pfizer Vaccine: Efficacy rate of 95%
Moderna Vaccine: Efficacy rate of 94%
Johnson & Johnson Vaccine: Efficacy rate of 72% in US trials
The Pfizer and Moderna vaccines require two doses about 1 month apart.
The Johnson & Johnson vaccine requires only one dose.
All vaccines take a couple of weeks to give any protection.
After the final dose of any of these vaccines, it takes about two weeks for the body to
build up full protection
Clinical Studies about COVID-19 Vaccines

50. Side Effects of COVID19 Vaccine
When the body’s immune system mounts a response to a natural infection OR
vaccination the result is local and/or systemic inflammation
Usually start within 24 to 36 hours and Go away after 24 to 48 hours.
More common in younger adults
Local inflammation: injection site soreness, redness, swelling
Systemic inflammation includes fever, muscle aches, headache, Fatigue
The stronger the immune response, the more prominent the side effects
The healthier the individual, the stronger the immune response.

51. CHW
Inform supervisor
COMMUNITY
CONTACTS
SEVERE SUSPECT
DIFFICULTY BREATHING
WEAR A MASK
MILD/MODERATE SUSPECT
1. New dry cough
AND
2. Fever
+ 2 OTHER SIGNS
Sore throat
Loss of taste or smell
Tiredness
Headache
Diarrhoea
Aching muscles
HEALTH CENTRE/HOSPITAL
TESTING AND CARE
SEVERE SUSPECT
DIFFICULTY BREATHING
WEAR A MASK
STAY AT HOME
Rest
Drink fluids
Paracetamol if feverish
Keep distance
Wash hands
Cough/Sneeze
Disinfect surfaces
CHW
Inform supervisor
Inform Testing Team
TESTING TEAM
takes sample
COVID-19 Algorithm
How to find and guide people with symptoms that look like COVID-19

52. THANK YOU
52