How “sensitive” is the PCR in diagnosing coronavirus/Covid-19?

A definite diagnosis of Covid-19 requires viral testing, usually through PCR performed on upper (nasopharyngeal or oropharyngeal) or lower respiratory samples (sputum, bronchoalveolar lavage [BAL] fluid). Rates of positive PCR may be affected by stage of the disease and/or its severity.
Nasopharyngeal sample: This seems to be the most practical and readily available means of confirming Covid-19 diagnosis, with positive rates of ~75% during the first 2 weeks of illness in patients considered to have severe disease. For patients with mild Covid-19, a positive PCR rate of 72% has been reported during the 1st week, dropping to 54% during the 2nd week (1).
Oropharyngeal sample: Lower positive PCR rates have been observed with throat swabs, as low as ~30% in mild Covid-19 during the 2nd week of the illness and ~60% in severe disease during the first week of illness (2).
Sputum: Sputum may have the highest positive rates ranging from ~75% in mild disease during the second week of illness to ~90% during the 1st week of severe disease. The problem with sputum sampling is that less than one-third of patients with Covid-19 can provide a sample given the usually dry nature of their cough (1,4).
BAL fluid: In a limited number of patients with severe disease who had bronchoalveolar lavage sampling during the 2nd week of illness, 3 (25%) of 12 patients with positive PCR on BAL had negative upper respiratory samples (1). So in severe disease, the virus definitely prefers to replicate in the lower respiratory tract.
Potential explanations for a negative PCR include low viral titers and specimen handling. So, in patients suspected of having Covid-19 based on clinical/laboratory/radiograph grounds, a negative upper respiratory sample, particularly oropharyngeal source, should not rule out this disease.


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1. Yang Y, Yang M, Shen C, et al. Evaluating the accuracy of different respiratory specimens in the laboratory diagnosis and monitoring the viral shedding of 2019-nCoV infections. MedRxiv. 2020. DOI:
2. Ai T, Yang Z, Hou H, et al. Correlation of chest CT and RT-PCR testing in Coronavirus disease 2019 (COVID-19) in China: A report of 1014 cases. Radiology 2020.
3. Bai HX, Hsieh B, Xiong Z, et al. Performance of radiologists in differentiaging COVID-19 from viral pneumonia on chest CT. Radiology 2020. 
4. Huang C, Wang Y, Li X, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet 2020.
Disclosures: The listed questions and answers are solely the responsibility of the author and do not necessarily represent the official views of Massachusetts General Hospital, Harvard Catalyst, Harvard University, its affiliate academic healthcare centers, or its contributors. Although every effort has been made to provide accurate information, the author is far from being perfect. The reader is urged to verify the content of the material with other sources as deemed appropriate and exercise clinical judgment in the interpretation and application of the information provided herein. No responsibility for an adverse outcome or guarantees for a favorable clinical result is assumed by the author. Thank you!

How “sensitive” is the PCR in diagnosing coronavirus/Covid-19?

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