COVID-19 – Sample collection guidelines

April 1, 2020

Indian Council of Medical Research – National Institute of Epidemiology

Scope of this document:
To be used by hospitals involved in collecting samples for COVID-19 testing


This document gives information on sample collection, packing and transport to laboratory for COVID-19 testing


 Clinician:
o To identify the appropriate patient for COVID-19 testing o To identify the appropriate specimen to be collected

 Lab technician
o Should have received appropriate training for sample collection from

suspected SARI/COVID-19 cases
o To collect appropriate samples as decided by the treating doctor
o To wear proper PPE as prescribed by NIV Pune
o To strictly follow biosafety measures during collection and packing of

samples and to follow the biomedical waste management guidelines for safe disposal of generated bio-waste.

Selection of patient for testing:

o Any Patient who satisfies the testing “Criteria for SARI/COVID-19” as prescribed by State or Central Government.

o Any patient identified by “As a suspected case of SARI/ COVID-19” the treating doctor

Details of sample collection materials and temperature during transport/ storage (till testing) of different samples from suspected SARI/ COVID cases.



Steps to follow-up during the sample collection:
1. Materials needed for the sample collection: (Nasal & Throat swab):

April 1, 2020



Description/Details (if any)

Cat no. (If any)


Viral transport medium (VTM) #




Polyester tipped plastic shaft swab *

Fisher Brand





Flocked Swab *


PW1172- 1X500NO


Ref 519CS01


Tongue depressor



Face mask




Disposable apron



Disposable Nitrile Gloves


Hand sanitizer

Alcohol based rub


Discard bag

Appropriate Biohazard Discard bag


Cool box

Thermocol box


Gel packs

To be frozen at -20oC prior use


Head cap




Reusable lab goggle


Brown tape

Sealing the sample box


Surgical spirit

Disinfect sample collection area


Cryo label

Sample Labelling

  # VTM Precautions: Ready to use VTM to be used within the expiry date. Always check for turbidity or any growth in VTM prior to use for sample collection or before dispatch of VTM to surveillance site. If any turbidity or growth is found, please discard the whole batch of VTM.

  *Use of cotton-tipped or calcium alginate swabs or swabs with wooden shafts is NOT RECOMMENDED.

2. Steps 1.


3. 4. 5.

6. 7. 8.

to be followed for specimen collection using aseptic method:
Nasal swab and/or throat swab specimens is to be collected as per GOI guidelines.
Sample collection area should be kept clean and table or work surface should be properly disinfected with surgical spirit.
Collect required details from the patient and fill the sample collection form. Ensure that patient is seated in a comfortable seating position.
Clearly explain the sample collection procedure to ensure full cooperation from the patient.
Wear appropriate personal protective equipment (PPE) such as gloves, apron, N95 mask, head cap, goggles before starting the procedure.
Label the specimen collection vial containing VTM with the unique participant/ sample ID.
Specimen should be collected under good illumination.


April 1, 2020

9. Throat/ oro-pharyngeal swab collection

a. Gently tilt the patient’s head back

b. Steady the chin

c. Ask the patient to open his/her mouth

d. Use a disposable tongue depressor to hold the tongue well

e. Insert a sterile swab

f. Swab both the tonsils and the posterior pharynx vigorously with a rotating motion, till the patient starts to gag

g. Remove the swab without touching the tongue.

h. The swab is then placed in the labelled tube containing VTM

i. The applicator stick is broken off at the indicated mark (if provided)
or at below the level of the tube opening

j. Close and tightly screw cap the tube.

10.Nasal swab collection

a. Take a fresh sterile swab

b. Gently tilt the patient’s head Backwards and steady the chin

c. Insert the swab into the nostril parallel (1-2 cm) to the palate until the
resistance is met at turbinate

d. Hold the swab in that position for few seconds and then withdraw
slowly in a firmly rotating motion (5 times clockwise and 5 times

11.Appropriate precautions should be taken in collecting specimens since this

may expose the lab technician/ sample collector to respiratory secretions

from the patient.
12.Specimens from both nostrils are obtained with the same swab vigorously,

irrespective of nasal congestion if any.
13. The nasal swab is placed in the same VTM tube containing throat swab. The

applicator stick is broken off as done for throat swab and the tube is screw

capped tightly.
14.The vial is then placed in the cool box containing tube rack in between the

frozen gel packs.

3. Sample handling at collection site:

1. A unique specimen ID is written/ pasted on each VTM sample by the lab

2. VTM containing samples are to be kept in cool box immediately after

3. VTM tube IDs are cross checked with the details in the filled sample
collection form.

4. If the specimens cannot be sent to the laboratory within specified time frame
(refer table on page 1), they should be stored at or below –70°C in ultra-low

5. Repeated freezing and thawing must be avoided.

4. Transportation of samples from field site to testing laboratory:
1. Samples should be transported at 2-8°C within specified time frame to the

testing laboratory.



April 1, 2020

2. Samples should be kept in proper standing position in appropriate test tube rack.

3. The VTM containing part of the tube should be in direct contact with frozen gel packs.

5. Precautions:

1. Always use personal protective equipment (PPE) e.g. Laboratory apron/
gown, face mask, gloves and goggles.

2. Wipe gloves thoroughly with a disinfectant (e.g., surgical spirit) before and
after taking the sample.

Current testing modalities for laboratory diagnosis of COVID-19

1. Real Time PCR testing is the recommended testing for COVID-19 diagnosis.

2. Viral RNA is extracted from the Nasal/ throat swab specimen in VTM.

3. Initial Screening RT PCR involves detection of ‘E’ gene (coding for SARS-
CoV-2 viral envelope)

4. Confirmation of samples positive in screening PCR involves detection of
one of the following two gene targets:

o RdRp gene (coding for SARS-CoV-2 RNA dependent RNA

o ORF gene (coding for SARS-CoV-2 Open Reading Frame)


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