Nigeria Centre for Disease

Control
Protecting the health of Nigerians

COVID-19 Sample
collection, packaging
and transport
NCDC LABORATORY PILLAR
 Learning
objectives
At the end of this learning session participants will be able to:
o Know the types of specimen required for diagnosis of COVID-19
o Understand how to collect clinical specimens
o Describe the specimen collection process
o Package and ship patient specimens from a referral site to the
testing laboratory

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 Introductio
n
• Samples should be collected for laboratory testing from patients who meet
the case definition

• Patients may present to health care facilities or be found through screening

at ports of entry

• Patients are also encouraged to present to health facility if they develop

symptoms within 14 days of recent travel to China or countries with ongoing
transmission, or exposure to health facility where confirmed patients are receiving
treatment

• All health care workers are encouraged to remain vigilant for respiratory illness
3 with unknown causes that NIGERIA
may warrant
CENTRE FORfurther testing if patient’s clinical signs
DISEASE CONTROL
 Interim national case
a) Suspecteddefinition
Case
• Any person (including severely ill patients) with any of the following symptoms: fever, cough or difficulty
in breathing who within 14 days before the onset of illness had any of the following exposures:
• History of travel to any country with confirmed and ongoing community transmission of SARS- CoV-2
OR
• Close contact with a confirmed case of COVID-19 OR

• Exposure to a healthcare facility where COVID-19 case(s) have been reported

b) Probable case
• A suspect case for whom testing for COVID-19 is inconclusive or for whom testing was positive on a
pan- coronavirus assay. All inconclusive tests will be referred to an expert laboratory for further testing

c) Confirmed case
• A person with laboratory confirmation of SARS-CoV-2 (COVID19) infection with or without signs and
symptoms
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 Recommended specimens to be
collected
• Patients that meet the case definition for suspected COVID-19 infection
should be tested for the virus via RT-PCR
For patients with mild disease:
• Nasal and throat swabs are recommended – each swab to be placed into
a single VTM
• Sputum (only to be collected if the patient has a productive cough)
• Post mortem samples (nasal and throat swabs can also be collected)
For severely ill patients:endotracheal aspirate or bronchoalveolar lavage
• Collect 2-3 mL into a sterile, leak-proof, screw-cap sputum collection cup
or sterile dry container. Refrigerate specimen at 2-4°C

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Specimen type Collection materials Transport to Storage till testing Comment
laboratory
Nasal swab Dacron or polyester flocked 2° to 4°C ≤5 days; 4°C Can be placed in the same VTM tube as
swab and VTM >5days; -20 to -70°Coropharyngeal swab;
Oropharyngeal swab Dacron or polyester flocked 2° to 4°C ≤5 days; 4°C Can be placed in the same VTM tube as
swab and VTM >5days; -20 to -70°Cnasopharyngeal swab
Sputum Sterile container 2° to 4°C ≤48 hrs; 4°C Ensure material is from lower respiratory tract;
>48hrs -20 to -70°C ensure adherence to IPC standards and correct
use of PPE
Bronchoalveolar Sterile container 2° to 4°C ≤48 hrs; 4C Collected from severely ill patient,
Lavage >48hrs -20 to -70°C Dry swab to be used if bacterial or fungal culture
is to be performed.
Ensure adherence to IPC standards and correct
use
of PPE
(Endo)tracheal Sterile container 2° to 4°C ≤48 hrs; 4°C Dry swab to be used if bacterial or fungal culture
aspirate, >48hrs -20 to -70°C is
nasopharyngeal to be performed.
aspirate or nasal Ensure adherence to IPC standards and correct
wash use of PPE

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 Materials needed for specimen
collection
• Personal Protective Equipment (PPE); • Falcon Tube,
gown, gloves, face mask/face shield, • Zip Lock Bags
N95 respirator, goggles
• Waste bags,
• Nasopharyngeal/nasal Swab disinfectants
• Oropharyngeal Swab • Case Investigation
• Viral Transport Medium (VTM) Forms

• Wooden tongue depressors • Permanent Marker

• Cool box • Digital Thermometer

• Ice packs • Scissors

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 US
E

DO NOT
Rayon tipped swabs (aluminum USE!!
shaft) for NP
Dacron tipped swabs, flexible for
OP (can also be used for NP)
calcium alginated
or cotton swabs or
those with
Polyester-fiber tipped wooden shafts.
swabs
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• Used for collection of specimens for virus isolation and molecular testing
• Essential for virus survival
• Prevents specimen from drying out = virus death
• Prevents bacteria and fungi growth
• Can be stored at 2-8°C for short periods (days)

• If VTM is not available swabs can be stored and shipped in absolute

(100%) ethanol.
• UTM Universal transport media is a suitable alternative

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For each selected patient who meets the case
definition:
• Protect yourself (PPE)
• Fill out a data collection form – must accompany specimen
• Label specimens appropriately (unique identifier, date, type of sample, age, gender)
• Take nasal and oropharyngeal swabs
• Place 2 swabs into a single VTM
• Collect sputum, if it can be produced
• Store labeled specimens in a refrigerator (2 to 4C) until they can be transported to
testing facility.
• Manage waste

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Protect yourself
(PPE)
Gloves

N-95 Mask

WASH Face shield

YOUR
HANDS
Gown
BEFORE AND
AFTER PATIENT
CONTACT AND goggles
BETWEEN
PATIENTS

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 Safety procedures during sample
• collection
HCWs performing aerosol-generating procedures (i.e. aspiration or open suctioning of
respiratory tract specimens, intubation, cardiopulmonary resuscitation, bronchoscopy) should
use additional precautions:
• Respirators (NIOSH-certified N95, EU FFP2 or equivalent, or higher level of protection).
• Eye protection (i.e. goggles or a face shield).
• Clean, long-sleeved gown and gloves.
• The procedures should be performed in an adequately ventilated room: at a minimum,
rooms with a natural ventilation air flow of at least 160L/s/, or negative pressure rooms with at
least 12 air changes per hour and a controlled direction of air flow when using mechanical
ventilation
• Limit the number of persons present in the room to the minimum required for the patient’s care
and support;
• Follow
12 appropriate steps for donning and CENTRE
NIGERIA doffingFOR
PPE to reduce
DISEASE CONTROL risk of infection
Nasal Swab
1. Insert a dry swab (polyester or dacron)
into the nostril in line with the palate.
2. Advance the swab tip past the
vestibule (anterior nares) to the nasal
mucosa
3. Gently rotate the swab to collect nasal
secretions from anterior portions of
the turbinate and septal mucosa.
4. Cut off the tip of swab into a vial
containing VTM
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 Specimen collection procedure
(2)
Oropharyngeal (Throat) Swab
1. Have the patient open mouth
wide open
2. use wooden tongue depressor
to depress the tongue
3. Swab the back of throat near
the tonsil
4. Put tip of swab into vial
containing Virus Transport
Medium (VTM)
5. Using scissors to cut the
applicator stick

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 Specimen collection procedure
(3)
Sputum
• Have the patient rinse the mouth with water and then
expectorate deep cough sputum directly into a sterile,
leak-proof, screw-cap sputum collection cup or sterile
dry container. Refrigerate specimen at 2-4°C

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Following specimen collection there will be items that require safe
disposal.

• If there are multiple patients;

• change gloves between each patient – do not reuse
gloves
• Options for safe disposal include:
• disinfection
• autoclaving if available
• incineration, bury

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 For specimens in VTM:
• Transport to laboratory as soon as possible

• Store specimens at 4°C (ice packs or refrigerator)

before and during transportation within 48 hours

• Store specimens at -70°C or liquid nitrogen > 48 hours

• Avoid freeze-thaw cycles

• Better to keep on ice for a week than to repeat
freeze and thaw

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 • Leak-proof primary receptacle containing the sample

• Leak-proof-rigid secondary container – 50mL falcon tube or Ziploc

bags

• Absorbent material

• Bio bottles

• Fiberboard box/Cool box

• Ice-packs

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Packaging and shipment to the
laboratory
• The labelled VTM tubes are to be
placed inside a falcon tube and then
into a bio- bottle
• If no bio bottle is available place the
falcon tube into a Ziploc bag
• Labelled Sterile containers for sputum or
bracheolavage samples can be placed
into a Ziploc bag and then into the bio-
bottle
• The bio-bottles are placed into the
giostyles with icepacks for transportation.
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States to lab
distribution
S/N STATES/REGION TESTING LABORATORY

1 NORTHERN REGION (NW, NE, NC) NCDC NRL, GADUWA, ABUJA

2 SOUTH WEST REGION LUTH, YABA, LAGOS

3 SOUTH EAST REGION NIMR, YABA, LAGOS

4 SOUTH SOUTH REGION ISTH, IRUA, EDO

5 SEQUENCING ACEGID, EDE, OSUN

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 Criteria for sample
rejection
• An un-labelled sample.
• A sample with duplicate ID
• Sample that contain less than 600ul of VTM on reception
• A sample that contains no swab
• Sample in a leaking container
• VTM containing sample with turbid appearance or color
change
• A sample without case investigation forms .
• Case investigation forms without samples
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SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected
Patients
https://www.nejm.org/doi/full/10.1056/NEJMc2001737

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