Specimen Collection and Testing for Coronavirus COVID-19

Updated: March 21, 2020 10:15 ET

Adapted from the U.S. Centers for Disease Control (CDC).[1]

Guidelines for Clinical Specimens

In the United States

  • Health care providers should contact their local/state health department immediately to notify them of patients with fever and lower respiratory illness who they suspect may have COVID-19.
  • Local and state public health staff will determine if the patient meets the criteria for testing for COVID-19.
  • The state and local health department will assist clinicians to collect, store, and ship specimens appropriately, including during afterhours or on weekends/holidays.
  • Clinical specimens should be collected for routine testing of respiratory pathogens at either clinical or public health labs.
  • Note that clinical laboratories should NOT attempt viral isolation from specimens collected from persons suspected to have COVID-19 unless this is performed in a biosafety level 3 (BSL3) laboratory.
  • Testing for other pathogens by the provider should be done as part of the initial evaluation but should not delay testing for COVID-19.

Specimen Type and Priority

Upper respiratory tract specimens

  • For initial diagnostic testing for COVID-19, CDC recommends collecting and testing an upper respiratory nasopharyngeal swab (NP).
  • Collection of oropharyngeal swabs (OP) is a lower priority and if collected should be combined in the same tube as the NP. Collection of only OP swab is acceptable if other swabs are not available.
  • Collection of sputum should only be done for those patients with productive coughs. Induction of sputum is not recommended.
  • Specimens should be collected as soon as possible once a PUI is identified, regardless of the time of symptom onset. Maintain proper infection control when collecting specimens.

Lower respiratory tract specimens

  • CDC also recommends testing lower respiratory tract specimens, if available.
  • For patients who develop a productive cough, sputum should be collected and tested for SARS-CoV-2. The induction of sputum is not recommended. For patients for whom it is clinically indicated (e.g., those receiving invasive mechanical ventilation), a lower respiratory tract aspirate or bronchoalveolar lavage sample should be collected and tested as a lower respiratory tract specimen.
  • Specimens should be collected as soon as possible once a PUI is identified, regardless of the time of symptom onset. Maintain proper infection control when collecting specimens.
  • See Biosafety FAQs for handling and processing specimens from suspected cases and PUIs.

COVID-19 Testing General Guidelines

  • Store specimens at 2-8°C and ship overnight to CDC on ice pack.
  • Label each specimen container with the patient’s ID number (e.g., medical record number), unique specimen ID (e.g., laboratory requisition number), specimen type (e.g., serum) and the date the sample was collected.
  • Complete a CDC Form 50.34 for each specimen submitted. In the upper left box of the form, 1) for test requested select “Respiratory virus molecular detection (non-influenza) CDC-10401” and 2) for At CDC, bring to the attention of enter “Stephen Lindstrom: 2019-nCoV PUI”.

I. Respiratory Specimens

A. Lower respiratory tract

Bronchoalveolar lavage, tracheal aspirate

  • Collect 2–3 mL into a sterile, leak-proof, screw-cap sputum collection cup or sterile dry container.

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.

B. Upper respiratory tract

Nasopharyngeal swab (NP) /oropharyngeal swab (OP)

  • Use only synthetic fiber swabs with plastic shafts. Do not use calcium alginate swabs or swabs with wooden shafts, as they may contain substances that inactivate some viruses and inhibit PCR testing. Place swabs immediately into sterile tubes containing 2-3 ml of viral transport media. In general CDC is now recommending collecting only the NP swab. If both swabs are used, NP and OP specimens should be combined at collection into a single vial. OP swabs remain an acceptable specimen type.
  • Nasopharyngeal swab: Insert a swab into nostril parallel to the palate. Swab should reach depth equal to distance from nostrils to outer opening of the ear. Leave swab in place for several seconds to absorb secretions. Slowly remove swab while rotating it.
    Oropharyngeal swab (e.g., throat swab): Swab the posterior pharynx, avoiding the tongue.

Nasopharyngeal wash/aspirate or nasal aspirate

  • Collect 2–3 mL into a sterile, leak-proof, screw-cap sputum collection cup or sterile dry container.

II. Storage

  • Store 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.

III. Shipping

For additional information, consultation, or the CDC shipping address, contact the CDC Emergency Operations Center (EOC) at 770-488-7100.

References

  1. Coronavirus Disease 2019 (COVID-19) Guidelines for Clinical Specimens. U.S. Centers for Disease Control and Prevention (CDC). Accessed March 21, 2020. [https://www.cdc.gov…]

Last updated: March 21, 2020