COVID-19: Diagnosis by PCR testing


Standard confirmation of acute SARS-CoV-2 infections is based on the detection of unique viral sequences by nucleic acid amplification tests (NAATs), such as real-time reverse-transcription polymerase chain reaction (RT-PCR). The assays’ targets include regions of the E, RdRP, N and S genes. PCR is the current “Gold Standard” test for the detection of SARS-Cov-2. 

Using nasal/throat swabs, samples are collected from symptomatic patients between days 1-5 from onset of symptoms. Respiratory secretions may be quite variable in composition, however, and the adequacy of sampling efforts may also vary. This can occasionally result in negative PCR results. In patients for whom SARS-CoV-2 infection is strongly suspected and upper respiratory tract swabs are negative, viral RNA may be detected in lower respiratory tract secretions, such as sputum or bronchoalveolar lavage. 

Detection of viral RNA by PCR may not equate with infectivity.  Infectious virus particles have been detected using cell culture systems but the relationship between the infectivity of a sample and the contagiousness of the patient is unclear. Viral load can, however, be a potentially useful marker for assessing disease severity and prognosis: a study indicated that viral loads in severe cases were up to 60 times higher than in mild cases. 

Lateral flow devices for the detection of SARS-CoV-2 antigen in respiratory samples have been developed and are being used for large scale testing. These have limited value due to their ease of use, but they have significantly reduced sensitivity compared to PCR and the quality control is deficient with a high test failure rate.