Detecting COVID-19 - method and pitfalls


-The test for current infection is RT-PCR - real-time reverse-transcription polymerase chain reaction (1)

-PCR allows rapid amplification and detection of DNA and RNA (1)

-Assays use a specific target within the viral genome to demonstrate presence or absence of SARS-CoV-2 (1)

-There are a range of potential targets used within different RT-PCR protocols, with some detecting multiple coronaviruses and some which only detect SARS-CoV-2 (2)

A list of currently available test protocols and their genomic targets is below (2): 

Source: WHO

The original viral genome for SARS-CoV-2, released for immediate public health support on 10th January, can be seen at the bottom of this page.

Clinical interpretation 

-Whilst there has not been systematic evaluation of SARS-CoV-2 tests, detection rates have been reported as around 60-70% using oropharyngeal and nasopharyngeal samples, based on findings from two non-peer reviewed studies of 213 and 490 patients (3)

-A data set of 610 patients found fluctuating positive and negative samples within affected patients, demonstrating false negatives occur. The authors proposed inadequate sample volumes, lab error or transportation issues as potential reasons for false negatives (4)

-A small study of 5 patients demonstrated that patients with CT findings suggestive of COVID-19 who initially tested negative for SARS-CoV-2 subsequently tested positive (5)

-A study of different sampling types has demonstrated highest detection rates in bronchoalveolar lavage fluid, followed by fibrobronchoscope brush biopsy, sputum, nasal swabs then pharyngeal swabs (6): 

Taken together, the results of these studies would suggest that serial testing from multiple sites over time is indicated in clinically suspected COVID-19 cases who test negative. Additionally, the overall clinical picture is more important than a single negative RT-PCR result. 


  1. Sarah Neidler. What are the differences between PCR, RT-PCR, qPCR, and RT-qPCR? [Webpage] Available from: [Accessed 30.3.20]

  2. WHO. Coronavirus disease (COVID-19) technical guidance: Laboratory testing for 2019-nCoV in humans [Webpage] Available from: [Accessed 30.3.20]

  3. Oxford COVID-19 Evidence Service. Accuracy of swabs for diagnosing COVID-19. [Webpage] Available from: [Accessed 30.3.20]

  4. Li Y et. al. Stability Issues of RT-PCR Testing of SARS-CoV-2 for Hospitalized Patients Clinically Diagnosed with COVID-19. J Med Virol. 2020 Mar 26. doi: 10.1002/jmv.25786. [Epub ahead of print]

  5. Xie X, Zhong Z, Zhao W, Zheng C, Wang F, Liu J. Chest CT for Typical 2019-nCoV Pneumonia: Relationship to Negative RT-PCR Testing. Radiology. 2020 Feb 12:200343. doi: 10.1148/radiol.2020200343. [Epub ahead of print]

  6. Wang W et. al. Detection of SARS-CoV-2 in Different Types of Clinical Specimens. JAMA. 2020 Mar 11. doi: 10.1001/jama.2020.3786. [Epub ahead of print]

Written by Dr Rachel Coles, Paediatric trainee, 30th March 2020

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