This document provides an epidemiological profile and overview of diagnostic methodologies for SARS-CoV-2. It discusses the first reported case in Wuhan, China in December 2019, describes the virus's transmission and stability on surfaces. Clinical features include fever, cough and shortness of breath, with severe cases progressing to pneumonia and ARDS. At risk groups are the elderly and those with pre-existing conditions. Diagnosis involves RT-PCR testing of nasopharyngeal or oropharyngeal swabs, with chest CT also useful. The document outlines sample collection, storage, and testing procedures.

1. EPIDEMIOLOGICAL PROFILE & DIAGNOSTIC
METHODOLOGIES OF SARS COV 2
PRESENTER : DR SOHAIL
MODERATOR : PROF. DR CHANDAN DAS
COVID-19

2. PNEUMONIA OF UNKNOWN ETIOLOGY IN WUHAN

3. ZERO CASE
 57 years old female, Wei Guixian.
 Shrimp seller in Wuhan city of China.
 On 10 December 2019 she developed cold, lethargy
 Fully recovered in January month

4. SARS-COV-2
 It’s a zoonotic virus.
 Bats appear to be the reservoir of COVID-19 virus.
 It belongs to large family of enveloped , positive strand of RNA viruses.
 Divided into 4 genera: alpha, beta, delta, and gamma
alpha and beta CoVs infect humans
 It is betacorona virus which has RNA dependant RNA polymerase.
 It enters human cells through ACE 2 receptors.

5. WORLDWIDE DISTRIBUTION

6. EPIDEMIC CURVE

7. COVID DATES
 12 December 2019: 1st case of COVID-19 reported in Wuhan city, Hubei province of China
 31 Dec’ 2019: Chinese authorities alerted WHO about cases of Pneumonia of unknown
etiology.
 01 Jan’ 2020: Wuhan Seafood Market closed by Chinese authorities.
 03 Jan’ 202: India notified by WHO regarding the outbreak
 07 Jan, nCoV identified as the causative organism
 12 Jan Wuhan’s First death due to Novel Corona Virus
 11 February 2020, WHO announced a name for the new coronavirus disease: COVID-19.
 11 March, 2020, the World Health Organization declared the COVID-19 outbreak a pandemic.
 As on 27 April, 213 countries affected. 2,810,325 confirmed cases, 193,825 deaths

8.  Mortality increases with age, with the highest mortality among people over 80 years of age (CFR 21.9%).
The CFR is higher among males compared to females (4.7% vs. 2.8%). By occupation, patients who
reported being retirees had the highest CFR at 8.9%. While patients who reported no comorbid
conditions had a CFR of 1.4%, patients with comorbid conditions had much higher rates: 13.2% for those
with cardiovascular disease, 9.2% for diabetes, 8.4% for hypertension, 8.0% for chronic respiratory
disease, and 7.6% for cancer.

9. FOUR EPIDEMIOLOGICAL AREAS
 In areas without cases,
the strategy in these areas is to "strictly prevent introduction". This includes quarantine arrangements in
transportation hubs, monitoring for temperature changes, strengthening of triage arrangements, use of fever
clinics, and ensuring normal economic and social operations.
 In areas with sporadic cases,
the strategy is focused on "reducing importation, stopping transmission and providing appropriate treatment".
 In areas with community clusters,
the strategy is focussed on "stopping transmission, preventing exportation, and strengthening treatment".
 In areas with community transmission,
the strictest prevention and control strategies are being implemented, the entry and exit of people from these
areas has been stopped and public health and medical treatment measures are comprehensively strengthened.

10. SUSPECT CASE

11. CONFIRMED CASE
 A person with laboratory confirmation of COVID-19
infection, irrespective of clinical signs & symptoms.

12. CONTACT
 A contact is a person who experienced any one of the following
exposures during the 2days before and the 14days after the onset
of symptoms of a probable or confirmed case :
1. Face to face contact with a probable / confirmed case within
1meter and for more than 15mins;
2. Direct physical contact with a probable / confirmed case;
3. Direct care for a patient with a probable / confirmed COVID-19
disease without using proper personal protective equipments;

13. CLINICAL FEATURES
 Uncomplicated illness : fever , cough , sore throat , nasal congestion , malaise , headache
 Mild pneumonia
 Severe pneumonia
 ARDS
 Sepsis
 Septic shock

14. CONTD…..

15. CONTD….
 ST segment elevation in COVID-19 (nejm)
 Neurological feature in severe SARS COV 2 (nejm)
1. Agitation
2. Confusion
3. Diffuse corticospinal signs, brisk DTR , ankle clonus
4. MRI brain s/o leptomeningeal enhancement & b/l frontotemporal
hypoperfusion
5. GBS

16. C/F IN CASES OF CHINA
3.7%
5.0%
11.0%
13.6%
13.9%
14.8%
18.6%
33.4%
38.1%
67.7%
87.9%
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
DIARROHEA
VOMITTING
CHILLS
HEADACHE
SORE THROAT
MAYALGIA
SHORTNESS OF BREATH
SPUTUM
FATIGUE
COUGH
FEVER

17. CYTOKINE STORM
 Cytokine storm (CS) refers to excessive and uncontrolled release of pro-inflammatory cytokines.
 Clinically, it commonly presents as systemic inflammation, multiple organ failure, and high inflammatory
parameters.
 In infectious diseases, CS usually originates from the focal infected area, spreading all over the body
through circulation.
 In COVID-19,accompanied by rapid virus replication, a large number of inflammatory cell infiltration and
CS led to acute lung injury, acute respiratory distress syndrome (ARDS) and death.
 In a study by immunologist in China, they measured cytokine levels in 41 inpatients (including 13 ICU
patients and 28 non ICU patients), IL-1B, IL-1RA, IL-7, IL-8, IL-9, IL-10, fibroblast growth factor (FGF),
granulocyte-macrophage colony stimulating factor (GM-CSF), IFNγ, granulocyte-colony stimulating
factor (G-CSF), interferon-γ-inducible protein (IP10), monocyte chemoattractant protein (MCP1),
macrophage inflammatory protein 1 alpha (MIP1A), platelet derived growth factor (PDGF), tumor
necrosis factor (TNFα), vascular endothelial growth factor (VEGF) were increased.

18. CONTD…
 Most of severe COVID-19 patients in our ICU ward had persistent very high
level of erythematosus sedimentation rate (ESR), CRP, and high level of IL-
6,TNFα, IL-1β, IL-8, IL2R, etc., and were associated with ARDS,
hypercoagulation and disseminated intravascular coagulation (DIC),
manifested as thrombosis, thrombocytopenia, gangrene of extremities.
 Autopsy findings revealed destruction of secondary lymphoid organs, spleen
atrophy, the number of lymph nodes decreased, diffuse alveolar damage in
lung.
 As we know that 2019-nCoV infects target cells through angiotensin
converting enzyme 2 (ACE2), while there was no ACE2 expression on
lymphocytes, we speculate that lymphocytes were probably destroyed by CS.

19. TRANSMISSION
 Infected droplets
>5µm, travel <1m
 Aerosols
<5µm, travel>1m
 Contact
Hands, surfaces

20. CONTD…
 Presymptomatic people are infectious.
 Patients may be infectious 1 to 3 days before symptom onset and that up
to 40 to 50% of cases may be attributable to transmission from asymptomatic
or presymptomatic people.
 Just before or soon after symptom onset, patients have high nasopharyngeal
viral levels, which then fall over the course of approximately 1 week.
 Patients with severe disease may shed the virus for longer periods
(Ref: nejm/corona)

22. AEROSOL & SURFACE STABILITY OF SARS COV 2
 Aerosol - 3hours
 Plastic - 72hrs
 Stainless steel - 48hrs
 Copper - 4hrs
 Cardboard - 24hrs
(Ref: nejm/corona)
Survivability outside body:
• 1-2 days on nonporous surfaces
• 8-12 hours on porous surfaces
• Currently this information on 2019-
nCoV not clear
Incubation period:
Current estimates of the incubation period of
SARS-CoV-2 range from 2-14 days.

23. RISK FACTORS
 Older age ( > 65 yrs)
 Chronic lung disease
 Cardiovascular disease
 Hypertension
 Diabetes mellitus
 Obesity
 End stage renal disease
 Immunocompromised state
 Liver disease
 Male gender*

24. AGE DISTRIBUTION OF CASES IN CHINA (N=72,314)
0-9
=0.9%
10-29 =9.3%
30-39 =17.0%
40-49 =19.2%
50-59 =22.4%
>60=31.2%
• Median age: 51 years
• Range= 2 days-100 years
• Males: 51%
• Health care workers: 3.8%
88% reported from Hubei

25. SEVERITY OF ILLNESS (N=72,314)
0
0.2
0.2
0.2
0.4
1.3
3.6
8
14.8
0 2 4 6 8 10 12 14 16
0-9
10--19
20-29
30-39
40-49
50-59
60-69
70-79
>=80
Case Fatality Rate (%)

26. LAB FINDINGS
 Lymphocytopenia
 High CRP
 High LDH & ferritin
 Raised D-dimer
 High procalcitonin
 High SGOT & SGPT levels

29. RAPID
ANTIBODY
BASED
BLOOD TEST

30. CANDIDATES FOR SAMPLE COLLECTION
 All symptomatic individuals who have undertaken international travel in the
last 14 days .
 All symptomatic contacts of laboratory confirmed cases .
 All symptomatic health care workers .
 All patients with Severe Acute Respiratory lllness (fever AND cough and/or
shortness of breath) .
 Asymptomatic direct and high-risk contacts of a confirmed case should be
tested once between day 5 and day 14 of coming in his/her contact.

31. SAMPLE COLLECTION
 Most important step in lab diagnosis
 A. Upper respiratory tract
Nasopharyngeal (NP) swab/oropharyngeal (OP) swab
 B. Lower respiratory tract
Bronchoalveolar lavage, tracheal aspirate, pleural fluid, lung biopsy

32. CONTD…
 Nasopharyngeal swab:
Insert flexible wire shaft minitip swab through the nares parallel to the palate (not upwards)
Swab should reach depth equal to distance from nostrils to
outer opening of the ear
Gently rub and roll the swab.
Leave swab in place for several seconds to absorb secretions.
Slowly remove swab while rotating it.

33. CONTD…
 Oropharyngeal swab (e.g., throat swab):
Insert swab into the posterior pharynx and tonsillar areas.
Rub swab over both tonsillar pillars and posterior oropharynx and avoid touching the
tongue, teeth, and gums.
 Combined nasal & throat swab:
Tilt patient’s head back 70 degrees. While gently rotating the swab, insert swab less than
one inch into nostril (until resistance is met at turbinates). Rotate the swab several times against
nasal wall and repeat in other nostril using the same swab. Place tip of the swab into sterile viral
transport media tube and cut off the applicator stick. For throat swab, take a second dry
polyester swab, insert into mouth, and swab the posterior pharynx and tonsillar areas (avoid the
tongue). Place tip of swab into the same tube and cut off the applicator tip.

34. 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.

35. RT-PCR DIAGNOSTIC PANEL
 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 coronaviruses as well as
specific detection of the 2019-nCoV;
 RP primers and probes that target the Human RNase P gene; and
 nCoVPC, the 2019-nCoV positive control used in the assay.

36. SENSITIVITY & SPECIFICITY
 SENSITIVITY
For the nCoV_IP and E_Sarbeco real-timeRT-PCR Sensitivity, in terms of 95% hit
rateis about 100 copies of RNAgenome equivalent per reaction (thisamount of target
sequences is always detected), the probability to detect lower amountsof virus
decreases, but samples containing 10 copies could be detectedwithmultiplex assay.
 SPECIFICITY
Cross-reactivity with other respiratory viruses was tested withspecimens known to be positive for
a panel of respiratory viruses (influenza A(H1N1)pdm09, A(H3N2), B-Victoria, B-
Yamagata; influenzaC; RSV A, B; hBoV; hPIV; hMPV; HRV/enterovirus; adenovirus; hCoV
(HKU1, OC43, 229E and NL63); MERS-CoV. None of the tested viruses showed reactivity
with PCR2 and PCR4.

37. ROLE OF CT CHEST
 Chest CT has been suggested to possess the potential to diagnose COVID-19
with significant sensitivity & even screen asymptomatic patient.
 Sensitivity – 97%
Specificity – 25%
 Chest CT is necessary even if RT PCR is negative