COVID-19 (SARS-CoV-2) PCR assay
Coronavirus disease 2019 (COVID-19) is a respiratory tract infection caused by a newly emergent coronavirus – Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) – which was first recognised in Wuhan, Hubei Province, China, in December 2019. Genetic sequencing of the virus suggests that SARS-CoV-2 is a betacoronavirus closely linked to SARS coronavirus.
Infectivity is now recognized to occur before the onset of symptoms and yet high titres of virus can be detected on upper airway surfaces in people who do not develop symptoms.
Infection with SARS-CoV-2, an RNA virus, is diagnosed using reverse-transcriptase PCR. The assays used at TDL show a minimum sensitivity of 98% and a specificity of 100%, with no cross-reactivity with other viruses.
The majority of people with COVID-19 have uncomplicated or mild illness (81%), with non-specific symptoms such as fever, fatigue, cough (with or without sputum production), anorexia, malaise, muscle pain, sore throat, dyspnea, nasal congestion, or headache. Rarely, patients may also present with diarrhoea, nausea and vomiting. Loss of taste and smell has been reported early in the infection.
A relatively small proportion of people, particularly but by no means exclusively in those aged >70 years, will develop severe illness requiring oxygen therapy (14%) and approximately 5% will require intensive care unit treatment. Time from the onset of the infection to hospitalisation can be up to ~13 days. Of those critically ill, most will require mechanical ventilation. The most common diagnosis in severe COVID-19 patients is severe pneumonia; this can progress to acute respiratory distress syndrome, and life-threatening multi-organ dysfunction and death. Mortality has been estimated at between 1 and 2% of those infected, the higher figure in men.
Limitations and clinical interpretation
As with all viral PCR assays, patients with very low viral loads are less likely to be detected. Negative (or ‘NOT detected’) results do not preclude infection with the SARS- CoV-2 virus and should not be the sole basis of a patient treatment/management or public health decision. Where there is a strong clinical suspicion of an early COVID-19 infection repeat sampling should be considered 24-48 hours later.
Patients with COVID-19 symptoms in intensive care have been shown to no longer carry the virus in the upper respiratory tract. Viral detection tests should assist in the decision on when to discontinue additional precautions for hospitalised patients. Results should be interpreted by a trained professional in conjunction with the patient’s history and clinical signs and symptoms, and epidemiological risk factors.
Detection of viral RNA by PCR does not equate with infectivity, unless infectious virus particles have been confirmed through virus isolation and cultured from the particular samples. 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.
Current PCR assays are able to detect all known SARS CoV-2 variants to date.
- Grant P, et al. Extraction-free COVID-19 (SARS-CoV-2) diagnosis by RT-PCR to increase capacity for national testing programmes during a pandemic. BioXriv 8 April 2020.
- European Centre for Disease Prevention and Control. Coronavirus: Infection. Accessed 6 October 2020.
|COVID-19 (SARS-CoV-2) RNA by PCR|