1. SARS-CoV-2
AN
OVERVIEW OF
LABORATORY DIAGNOSIS

2. Key Considerations on Modes of SARS-CoV-2
Transmission
• Person-to-person considered predominant mode of transmission, likely via respiratory droplets
from coughing, sneezing, or talking[1,2]
• High-level viral shedding evident in upper respiratory tract[3,4]
• Airborne transmission suggested by multiple studies, but frequency unclear in absence of
aerosol-generating procedures in healthcare settings[2]
• Odds that a primary case transmitted SARS-CoV-2 in an enclosed environment 18.7 x higher
compared with odds of estimated transmission rates in an open-air environment (95% CI: 6.0-
57.9)[1]
1. https://www.cdc.gov/coronavirus/2019-ncov/prevent-getting-sick/how-covid-spreads.html 2. WHO. Scientific Brief. July 9, 2020.
3. Wölfel. Nature. 2020;581:465. 4. Zou. NEJM. 2020;382:1177.
5. WHO. Scientific Brief. June 17, 2020. 6. ACOG. Practice Advisory: Novel Coronavirus 2019 (COVID-19). Last updated July 1, 2020. Slide credit: clinicaloptions.com

3. Proposed Routes of SARS-CoV-2 Transmission
Galbadage. Front Public Health. 2020;8:163. WHO. Scientific Brief. July 9, 2020. Slide credit: clinicaloptions.com
SARS-CoV-2–
Infected Host
Susceptible
Host
Aerosols
< 5 µm diameter
Suspended in air
Contact/Droplet
> 5 µm diameter
Direct contact
or
< 1 meter distance
Fomites (?)
Environmental
Stability
Points of entry:
Eyes, nose, or
mouth
Airborne (?)
> 1 meter distance
Urine/feces:
RNA found in
both; live virus
cultivated from
few specimens

4. Primary Symptoms of COVID-19
Li. J Med Virol. 2020;92:577.
https://www.cdc.gov/coronavirus/2019-ncov/symptoms-testing/symptoms.html Slide credit: clinicaloptions.com
Headache
Congestion or runny nose,
new loss of taste or smell
Fatigue, muscle
or body aches,
fever or chills
Nausea or
vomiting, diarrhea
Cough, sore throat
Shortness of breath
or difficulty breathing
“Symptoms may
appear 2-14 days
after exposure to
the virus”

5. SARS CoV2– Laboratory Diagnosis
5

6. Objectives of Laboratory Detection
Test , Trace and Treat
• Infected patients (high risk groups)may become seriously ill if not monitored closely
• Treatment needs to be tailored on a case to case basis
• Infected patients need to be isolated (contagious disease) to prevent further transmission
of disease
• Initiate contact tracing ( close contacts ) - may be asymptomatic carriers and assess need to
quarantine
• Identify when to discharge from isolation**

7. Whom to test? Strategy for COVID-19 testing in India(Version 5, dated 18/05/2020)
• All symptomatic (ILI symptoms) individuals
• All symptomatic (ILI symptoms) contacts of laboratory confirmed cases.
• All symptomatic (ILI symptoms) health care workers / frontline workers involved in
containment and mitigation of COVID19.
• All patients of Severe Acute Respiratory Infection (SARI).
• Asymptomatic direct and high-risk contacts of a confirmed case to be tested once
between day 5 and day 10 of coming into contact.
•Asymptomatic patients undergoing major surgical procedures
•No emergency procedure (including deliveries) should be delayed for lack of test. However,
sample can be sent for testing if indicated as above simultaneously.

9. Samples to collect?
• Nasopharyngeal swab
• Oropharyngeal swab
• Sputum
• Broncho-alveolar lavage
• Endo-tracheal secretions
• Under study: Nasal swab (self collection), Saliva (self collection)
• Antibody : Blood in EDTA

10. Nasopharyngeal swab

11. Oropharyngeal swab

14. Rapid Point-of-Care (PoC) Antigen Detection Test :
• Super-quick result in 15 minutes – HIGHLY SPECIFIC -95-97%
• ANTIGEN POSITIVE = CONFIRMED POSITIVE
• Does not need any special biosafety measures for test processing
• Does not need elaborate infrastructure
• Minimal staff training to perform , Simple to interpret
• Limitations: Moderately sensitive

15. ICMR recommends deployment of the rapid antigen
PoC test in the following settings:
• All containment zones identified by the State Governments,
• All Central & State Government Medical Colleges and Government
hospitals
• All private hospitals approved by National Accreditation Board for
Hospitals & Healthcare (NABH).
• All private labs accredited by National Accreditation Board for
Laboratories (NABL) and approved by ICMR as COVID-19 testing labs.
Sion hospital has round-the-clock Antigen testing in the booth and Elab

19. Real Time RT-PCR
This is the gold standard test for detecting cases of COVID-19.
• The test requires specialized laboratory setup with specific biosafety
• Average time taken is around 4-5 hours
• Very sensitive and highly specific, but sample collection errors can give false
negative results
• Symptomatic antigen-negative should be confirmed by RTPCR
•

20. Real time/ Quantitative
Reverse Transcriptase Polymerase Chain Reaction

21. Viral Transport Medium - VTM

24. The TrueNat and CBNAAT
• CBNAAT: Cartridge Based Nucleic Acid Amplification Testing
• These platforms have a quick turnaround time (30 -60 minutes) but
only 1-4 samples can be tested in one run, limiting the maximum
numbers that can be tested to 24-48 samples
• The viral lysis buffer that comes with the COVID-19 cartridges
inactivates the virus and poses minimum biosafety hazard. Safety is
further augmented by the closed nature of these platforms and
minimum sample handling.
• Very expensive*

30. IgG Antibody (Only for surveillance and not diagnosis):
IgG antibodies generally start appearing after two weeks of onset of infection, once the
individual has recovered after infection and last for several months. Therefore, the IgG test is
not useful for detecting acute infection.
However, detection of IgG antibodies for SARS-CoV-2 may be useful in the following situations:
• Serosurveys to understand the proportion of population exposed to infection with SARS-CoV-2
including asymptomatic individuals. Depending upon the level of seroprevalence of infection,
appropriate public health interventions can be planned and implemented for prevention
• Survey in high risk or vulnerable populations (health care workers, frontline workers,
immunocompromised individuals, individuals in containment zones etc) to know who has
been infected in the past and has now recovered
• identify convalescent plasma donors
• evaluate immune response to candidate vaccines

31. Summary
• Rapid Ag based assays are now available and highly useful in symptomatic
patients
• RT-PCR based assays are the gold standard diagnostic tests
• The tests are useful in the first week of illness and two days before onset
(pre-symptomatic / asymptomatic)
• Sample collection preferably from upper respiratory tract
• If result is negative, repeat a fresh specimen after 24-48 hrs
• Antibody based assays are not meant for diagnosis