Sample Collection, Storage

& Safe Transportation of

Specimens

Dr Afreenish Amir
Medical Microbiologist
National Institute of Health
Islamabad
 SAMPLE
COLLECTION
 1. Successful lab diagnosis of
• Why is the proper infection begins with collection
collection/transportation
of specimens important? 2. Ensure that specimen represent
the disease process; proper
following of standard protocol is
important

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The result of any laboratory examination is only as good
as the sample received in the laboratory
•The decision to test should be based on clinical and
epidemiological factor.
•PCR testing of asymptomatic or mildly symptomatic contacts can
be considered in the assessment of individuals who have had
contact with a COVID-19 case.

•Rapid collection and testing of appropriate specimens from

patients is a priority for clinical management and outbreak control.
•Suspected cases should be screened for the virus with nucleic acid
amplification tests (NAAT), such as RT-PCR.
 Biosafety Principles

To protect

1) People/patients
2) Yourself
3) Environment
 Biosafety: protect the people/patient

 Use single use /sterile equipment

 Work in a clean, dedicated area
 Disinfect
 Biosafety: protect yourself

Use Personal Protective Equipment

(PPE)

 Disposable Gloves
 Laboratory Coats / Gown
 Mask
 Protective Eyewear
 Biosafety: protect yourself

 Collect sharps immediately to prevent needle-stick injury

 Have first aid kit readily accessible
 Do not reuse contaminated equipment
 Biosafety: Protect Environment

 Decontaminate spills
 Place waste in leak-proof biohazard bags
 Ensure safe final management of waste
 Disinfect working areas for future use
 Sample collection
Materials Needed
1
•Dacron or polyester flocked swabs
•Tongue depressor (for Oropharyngeal swab)
•Vial with Viral Transport Medium (VTM)
•Pen/marker
•Disposable gloves
•Disposable gown
•N95 mask
•Goggles or face shield
•Specimen transport container with ice packs
•Specimen label and form
•Biohazard bags
• Tissues
•Soap and water
•Hand sanitizer
•Disinfectant
•All procedures should be undertaken
based on a risk assessment.
•Specimen handling for molecular
testing would require BSL-2 facilities.
•Attempts to culture the virus require
BSL-3 facilities at minimum.
Specimens to be collected
At minimum, respiratory material should be
collected:

Upper respiratory specimens: nasopharyngeal and

oropharyngeal swab or wash in ambulatory patients

and/or Lower respiratory specimens: sputum (if

produced) and/or endotracheal aspirate or
bronchoalveolar lavage in patients with more severe
respiratory disease.

(Note high risk of aerosolization; adhere strictly to

infection prevention and control procedures).
 COVID-19
Swab and VTM
•Nasopharyngeal (NP) and
Oropharyngeal (OP) swabs should
be collected as soon as possible
•The NP swab for VTM should be
collected first, followed by the OP
swab
•Both swabs will be placed in the
same vial of VTM

•Note: Placing the NP & OP swabs in

the same tube increases the viral
yield.
Nasopharyngeal swab
•Explain the procedure to the patient.
•Position patient in a comfortable position. Tilt the patient’s head back at
a 70-degree angle.
•Remove the swab from its protective package.
•Insert the swab into one nostril horizontally (not upwards) and continue
along the floor of the nasal passage for several centimeters until
reaching the nasopharynx (resistance will be met). (The distance from the
nose to the ear gives an estimate of the distance the swab should be inserted)
•Do not force the swab. If obstruction is encountered before reaching
the nasopharynx, remove the swab and try the other side.
Nasopharyngeal swab

•Rotate the swab gently through 180 degrees to make sure adequate
specimen is obtained. Leave the swab in place for 2-3 seconds to
ensure absorbance of secretions.

•Remove swab and immediately place into vial with VTM by inserting
the swab at least ½ inch below the surface of the media. Cut the excess
swab handle to fit the transport medium vial and reattach the cap
securely.
Oropharyngeal swab

•Ask the patient to open his/her mouth.

•Press the outer two-thirds of the tongue down with a tongue
depressor, making the tonsils and the posterior wall of the throat
visible.
•Insert swab, avoiding touching the teeth, tongue, or the
depressor.
•Rub the swab over both tonsillar pillars and posterior
oropharynx. This will cause the patient to gag briefly.
Oropharyngeal swab

•Place the swab into the vial containing VTM.

•Cut the excess swab handle to fit the transport medium vial
and reattach the cap securely.
• Carefully label specimen with patient ID number, and date
and time of specimen collection.
•Place specimen in cool box on ice.
 Labeling specimens

1. Name (unique identifier)

2. Type of specimen
3. Date, time and place of collection
4. Name/initials of the person responsible for collection

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 Sample transportation of suspected
2019 NCoV samples
•Transfer specimen with tracking log to the laboratory as
soon as possible.
•Ensure that personnel who transport specimens are trained
in safe handling practices and spill decontamination
procedures.
•Follow the requirements in the national or international
regulations for the transport of dangerous goods (infectious
substances) as applicable.

Notify the National Reference laboratory

(Department of Virology, PHLD, NIH Islamabad)
as soon as possible that the specimen is being
transported.
•Ensure good communication with the laboratory
and provide needed information.
•Alerting the laboratory before sending specimens
encourages proper and timely processing of
samples and timely reporting.
•Specimens should be correctly labelled and
accompanied by a diagnostic request form
Specimen Transport and Storage
Serological
testing

•Paired serum samples (in the acute and

convalescent phase) could support diagnosis once
validated serology tests are available.
•Cross reactivity to other coronaviruses can be
challenging, but commercial and non-commercial
serological tests are currently under development.
SAMPLE TRANSPORT/
SHIPMENT
 Dangerous Goods Classes

Class 2: Non-flammable non-toxic gases (Liquid nitrogen)

Class 3: Flammable liquids (Ethanol)
Class 6: Toxic and infectious substances
Division 6.1 addresses toxic substances
Division 6.2 addresses infectious substances
Class 9: Miscellaneous dangerous goods (Dry ice Genetically
modified microorganisms and organisms (not classified under
6.2)
 Category A: Infectious substances

An infectious substance which is transported in a form that, when

exposure to it occurs, is capable of:

 causing permanent disability,

 life-threatening or fatal disease in otherwise healthy humans or

animals.
 Substance Category (Division 6.2)
Category A (Infectious Substances)

– e.g. Ebola virus, Bacillus anthracis (culture only)

Category B (Biological Substances)

– e.g. Bacillus anthracis (patient specimen)

Exempt

– Medical assessment has determined a minimal likelihood that

pathogens are present e.g.
Pregnancy test, Drug screening
 Triple Packaging
Triple packaging provides three layers of containment to
protect the substances being shipped.

These layers are primary, secondary, and outer containers.

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 UN Specification Marking

An indication of the type of outer packaging (in this example a

3 An indication that the packaging has
passed a series of tests to ensure that
2 fibreboard box (4G); other examples include a solid plastic box it meets the requirements for
(4H2), or a plastic drum (1H2), applicable to dry shippers) Category A infectious substances
(Class 6.2)
Pressure test at 95 kPa Drop test
from 9 m Puncture test at 7 kg
Stacking test
The United Nations
1 packaging symbol
4G/Class 6.2/13
GB/2470

The last two digits of the year of

5 The country code of the competent state authority 4 manufacture (in this example 2013)
that has authorized the allocation of the mark (in
this example GB, signifying Great Britain)

The manufacturer’s code specified by the competent

6 authority (in this example 2470)
 Markings and Labels
Only Cat. A

Infectious
Substance Label

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 Markings and Labels
Only Cat. A
Orientation Labels
Mandatory on opposite sides when primary
container exceeds 50 ml

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 Markings and Labels
Only Cat. A

Emergency Contact
Name and Number

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 Markings and Labels
Only Cat. A

UN Specification
Marking

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THANK YOU