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National guidelines concerned with laboratory handling and testing of specimens from suspected,
COVID-19 patients.
Collecting and Handling Specimens Safely
For healthcare providers collecting specimens or working within 6 feet of patients suspected to be

infected with SARS-CoV-2, maintain proper infection control and use recommended personal protective
equipment (PPE), which includes an N95 or higher-level respirator (or facemask if a respirator is not
available), eye protection, gloves, and a gown.
Respiratory Specimen Collection
Respiratory specimens should be collected as soon as a decision has been made to test someone,
regardless of the time of symptom onset. The guidance below addresses options for collecting
specimens.
A. Upper respiratory tract
Nasopharyngeal specimen (NP) collection /Oropharyngeal (OP) (throat) specimen collection
collecting an NP specimen
 Tilt patient’s head back 70 degrees.
 Gently and slowly insert a minitip swab with a flexible shaft (wire or plastic) through the nostril
parallel to the palate (not upwards) until resistance is encountered or the distance is equivalent
to that from the ear to the nostril of the patient, indicating contact with the nasopharynx.
 Gently rub and roll the swab.
 Leave swab in place for several seconds to absorb secretions.
 Slowly remove swab while rotating it. Specimens can be collected from both sides using the
same swab, but it is not necessary to collect specimens from both sides if the minitip is
saturated with fluid from the first collection.
 If a deviated septum or blockage create difficulty in obtaining the specimen from one nostril, use
the same swab to obtain the specimen from the other nostril.
 Place swab, tip first, into the transport tube provided.
collecting an OP specimen
 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.
 Place swab, tip first, into the transport tube provided.
B. Lower respiratory tract

Bronchoalveolar lavage, tracheal aspirate, pleural fluid, lung biopsy (generally performed by a
physician in the hospital setting)
 Collect 2-3 mL into a sterile, leak-proof, screw-cap sputum collection cup or sterile dry
container.
 Due to the increased technical skill and equipment needs, collection of specimens other than
sputum from the lower respiratory tract may be limited to patients presenting with more severe
disease, including people admitted to the hospital and/or fatal cases.
Handling Bulk-Packaged Sterile Swabs Properly for Upper Respiratory Specimen Collection
Sterile swabs for upper respiratory specimen collection may be packaged in one of two ways:
 Individually wrapped (preferred when possible)
 Bulk packaged
When individually wrapped swabs are not available, bulk-packaged swabs may be used for specimen
collection; however, care must be exercised to avoid SARS-CoV-2 contamination of any of the swabs in
the bulk-packaged container.
 Before engaging with patients and while wearing a clean set of protective gloves, distribute
individual swabs from the bulk container into individual sterile disposable plastic bags.
 If bulk-packaged swabs cannot be individually packaged:
o Use only fresh, clean gloves to retrieve a single new swab from the bulk container.
o Close the bulk swab container after each swab removal and leave it closed when not in
use to avoid accidental contamination.
o Store opened packages in a closed, airtight container to minimize contamination.
o Keep all used swabs away from the bulk swab container to avoid contamination.
 As with all swabs, only grasp the swab by the distal end of the swab, using gloved hands only.
 When patients are self-collecting swabs under clinical supervision:
o Hand a swab to the patient only while wearing a clean set of protective gloves.
o The patient can then self-swab and place the swab in transport media or sterile
transport device and seal.
o If the patient needs assistance, you can help the patient place the swab into transport
media or a transport device and seal it.
Storing and Shipping Respiratory Specimens
Store respiratory 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. Pack and ship suspected and confirmed SARS-CoV-2
patient specimens. Personnel must be trained to pack and ship according to the regulations and in a
manner that corresponds to their function-specific responsibilities.
https://www.cdc.gov/coronavirus/2019-ncov/lab/guidelines-clinical-specimens.html
National guidelines concerned with laboratory handling and testing of specimens from probable,
COVID-19 patients.
Monitoring of contacts of probable and confirmed cases (annex 1)
- Contacts should be monitored for 14 days from the last unprotected contact.
- Contacts should self-limit travel and movements. Monitoring by public health authorities can be done
through household or virtual visits or by telephone to check for symptoms.
- Any contact who becomes ill and meets the case definition becomes a suspect case and should be
tested.
- Any newly identified probable or confirmed cases should have their own contacts identified and
monitored.
https://apps.who.int/iris/bitstream/handle/10665/330857/WHO-2019-nCoV-SurveillanceGuidance-
2020.3-eng.pdf?sequence=1&isAllowed=y
National guidelines concerned with laboratory handling and testing of specimens from confirmed,
COVID-19 patients.
All clinical specimens may contain potentially infectious materials. Precautions should be taken when
handling specimens suspected or confirmed to be positive for SARS-CoV-2, the virus that causes COVID-
19. Timely communication between clinical and laboratory staff is essential to minimize the potential
risk of handling specimens from patients with possible SARS-CoV-2 infection. These specimens should be
labeled accordingly, and the receiving laboratory should be alerted to ensure proper specimen handling.
General and specific biosafety guidelines for handling SARS-CoV-2 specimens are provided below.
General Guidance
All laboratories should perform a site-specific and activity-specific risk assessment to identify and
mitigate risks. Risk assessments and mitigation measures are dependent on:
 The procedures performed

 Identification of the hazards involved in the process and procedures
 The competency level of the personnel who perform the procedures
 The laboratory equipment and facility
 The resources available
when handling clinical specimens, all of which may contain infectious materials. Standard Precautions
include hand hygiene and the use of specific personal protective equipment (PPE) determined by the
potential for exposure to blood, body fluids, and infectious material. PPE, such as laboratory coats or
gowns, gloves, eye protection, or a disposable mask and face shield, can help protect the skin and
mucous membranes of the eyes, nose, and mouth.
Routine Diagnostic Testing
Routine diagnostic testing procedures, such as the following activities, can be handled in a BSL-2
laboratory using Standard Precautions:
 Initial processing of specimens

 Using automated instruments and analyzers
 Staining and microscopic analysis of fixed smears
 Examination of bacterial cultures
 Pathologic examination and processing of formalin-fixed or otherwise inactivated tissues
 Molecular analysis of extracted nucleic acid preparations
 Final packaging of specimens for transport to diagnostic laboratories for additional testing
(specimens should already be in a sealed, decontaminated primary container)
 Using inactivated specimens, such as specimens in nucleic acid extraction buffer
 Performing electron microscopic studies with glutaraldehyde-fixed grids
 Performing routine antibody or antigen detection tests
Decentralized and Point-of-Care Testing
Point-of-Care (POC) tests are intended to supplement laboratory testing or extend testing to
communities and populations that cannot readily access laboratory testing. In addition, POC testing
helps address emerging outbreaks quickly.
Virus Isolation
Virus isolation in cell culture and initial characterization of viral agents recovered in cultures of SARS-
CoV-2 should be conducted in a BSL-3 laboratory using BSL-3 practices. To determine appropriate
biosafety mitigation measures, laboratories should perform an activity-specific biosafety risk assessment
that evaluates laboratory facilities, personnel and training, practices and techniques, safety equipment,
and risk mitigation measures. Biosafety professionals, laboratory management, and scientific and safety
experts should be involved in the risk assessment process
Decontamination
Decontaminate work surfaces and equipment with an appropriate EPA-approved disinfectant for use
against SARS-CoV-2external icon. Follow manufacturer’s recommendations for disinfectant use, such as
dilution, contact time, and safe handling.
https://www.cdc.gov/coronavirus/2019-ncov/lab/lab-biosafety-guidelines.html

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National guidelines concerned with laboratory handling and testing of specimens from suspected,

Collecting and Handling Specimens Safely

For healthcare providers collecting specimens or working within 6 feet of patients suspected to be

Respiratory Specimen Collection

A. Upper respiratory tract

Nasopharyngeal specimen (NP) collection /Oropharyngeal (OP) (throat) specimen collection

 Tilt patient’s head back 70 degrees.

 Gently rub and roll the swab.

 Leave swab in place for several seconds to absorb secretions.

 Place swab, tip first, into the transport tube provided.

 Insert swab into the posterior pharynx and tonsillar areas.

 Place swab, tip first, into the transport tube provided.

B. Lower respiratory tract

 Individually wrapped (preferred when possible)

 If bulk-packaged swabs cannot be individually packaged:

o Store opened packages in a closed, airtight container to minimize contamination.

 When patients are self-collecting swabs under clinical supervision:

Storing and Shipping Respiratory Specimens

Monitoring of contacts of probable and confirmed cases (annex 1)

 The procedures performed

 Initial processing of specimens

Decentralized and Point-of-Care Testing

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