Currently the standard testing for SARS-CoV-2 is done by PCR-RT (reverse transcriptase polymerase chain reaction)

Respiratory viruses are best isolated from material that contains infected cells and secretions. Therefore, swabs should aim to brush cells and secretions off the mucous membranes of the upper respiratory tract.

Good specimen quality (i.e. containing sufficient cells and secretions) and appropriate packaging and transport (i.e., to keep virus viable/detectable) are essential.

Collecting a good quality specimen is vital

1. Upper respiratory tract specimen for all patients

A single nasopharyngeal swab is the preferred sample type. When not possible, a single nasal mid-turbinate swab, nasal or oropharyngeal swab may be collected

Transport and store swabs in universal/viral transport medium (UTM) or sterile saline, between 2-8°C. If UTM is not available, use dry swabs in a sterile tube. Dry swabs can be sent at ambient temperature, but must reach the laboratory within 2 days

2. Lower respiratory tract specimen when available

Sputum (if produced – do NOT induce), tracheal aspirates or bronchoalveolar lavage

Transport in standard specimen container. Does not require UTM Note: lower respiratory tract samples may have higher sensitivity than upper respiratory tract samples and should additionally be collected for severe cases

Timing of the specimen:

The typical time of onset of symptoms of COVID-19 is 5 days.

Source: BERLIN (NEJM)

The probability of a false-negative result in an infected person is:

  • 100% on day one (95% CI, 100% to 100%)

  • 67% on day four (CI, 27% to 94%)

  • 38% on day five (CI, 18% to 65%)

  • 20% on day 8 (CI, 12% to 30%)

  • 21% on day 9 (CI, 13% to 31%)

  • 66% on day 21 (CI, 54% to 77%)

Probability of having a negative RT-PCR test result given SARS-CoV-2 infection (top) and of being infected with SARS-CoV-2 after a negative RT-PCR test result (bottom), by days since exposure.

Source: Variation in False-Negative Rate of Reverse Transcriptase Polymerase Chain Reaction–Based SARS-CoV-2 Tests by Time Since Exposure

The sensitivity of the PCR-RT test is about 70%. This means that there is a 30% chance that the test if false negative (i.e. the person is infected with SARS-CoV-2 but tests negative).

Clinicians should not trust unexpected negative results. Assume a negative result is a “false negative” in a person with typical symptoms and known exposure.

The patient who has a high pre-test probability of testing positive, should be treated as a positive case even if the test is negative. They should quarantine for 14 days from onset of symptoms.

Read more here

What to do with a suspected false negative test:

You can repeat the test, or do a lower respiratory tract sample or chest imaging in severe cases of COVID-19.

For symptomatic patients with suspected COVID-19, WHO suggests using chest imaging for the diagnostic workup of COVID-19 when: (1) RT-PCR testing is not available; (2) RT-PCR testing is available, but results are delayed; and (3) initial RT-PCR testing is negative, but with high clinical suspicion of COVID-19.

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