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Laboratory Diagnosis

Last Updated: April 21, 2020


  • For intubated and mechanically ventilated adults who are suspected to have COVID-19 but who do not have a confirmed diagnosis:
    • The COVID-19 Treatment Guidelines Panel (the Panel) recommends obtaining lower respiratory tract samples to establish a diagnosis of COVID-19 over upper respiratory tract (nasopharyngeal or oropharyngeal) samples (BII).
    • The Panel recommends obtaining endotracheal aspirates over bronchial wash or bronchoalveolar lavage (BAL) samples when obtaining lower respiratory samples to establish a diagnosis of COVID-19 (BII).


Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses several diagnostic challenges, including potentially discordant shedding of virus from the upper versus lower respiratory tract. COVID-19 diagnosis is currently based on using a reverse transcriptase polymerase chain reaction (RT-PCR) assay to detect viral RNA in respiratory samples. The high specificity of RT-PCR removes the need for lower respiratory tract samples to diagnose COVID-19 when a nasopharyngeal swab is positive for a patient with recent onset of the disease. Lower respiratory tract specimens are considered by some experts to have higher yield, due to high viral load, consistent with what has been observed for severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS).1-7 Thus, lower respiratory tract samples should be obtained whenever possible if there is diagnostic uncertainty regarding COVID-19.

However, BAL and sputum induction are aerosol-generating procedures and should be performed only with careful consideration of the risk to staff of aerosol generation. Endotracheal aspirates appear to carry a lower risk of aerosolization than BAL and are thought by some experts to have comparable sensitivity and specificity to BAL specimens.


  1. Chan PK, To WK, Ng KC, et al. Laboratory diagnosis of SARS. Emerg Infect Dis. 2004;10(5):825-831. Available at:
  2. Wang W, Xu Y, Gao R, et al. Detection of SARS-CoV-2 in Different Types of Clinical Specimens. JAMA. 2020. Available at:
  3. Centers for Disease Control and Prevention. Evaluating and Testing Persons for Coronavirus Disease 2019 (COVID-19). 2020; Accessed April 8, 2020.
  4. Hase R, Kurita T, Muranaka E, Sasazawa H, Mito H, Yano Y. A case of imported COVID-19 diagnosed by PCR-positive lower respiratory specimen but with PCR-negative throat swabs. Infect Dis (Lond). 2020:1-4. Available at:
  5. Tang P, Louie M, Richardson SE, et al. Interpretation of diagnostic laboratory tests for severe acute respiratory syndrome: the Toronto experience. CMAJ. 2004;170(1):47-54. Available at:
  6. Memish ZA, Al-Tawfiq JA, Makhdoom HQ, et al. Respiratory tract samples, viral load, and genome fraction yield in patients with Middle East respiratory syndrome. J Infect Dis. 2014;210(10):1590-1594. Available at:
  7. Centers for Disease Control and Prevention. Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens from Persons Under Investigation (PUIs) for Middle East Respiratory Syndrome Coronavirus (MERS-CoV) – Version 2.1. 2020; Accessed April 8, 2020.