Current Knowledge
Molecular diagnostic tests such as nucleic acid amplification tests are the mainstay for diagnosing COVID-19. These tests detect viral RNA and are highly specific but cannot differentiate between viable and nonviable virus. A positive test result does not necessarily indicate that a person is infectious and requires isolation. The clinical sensitivity of NAATs is affected by the assay’s limit of detection, the time since infection began and the sample type. The most common sample type is nasopharyngeal swabs, but alternative sample sites such as anterior nares and saliva are being used more frequently due to patient discomfort and the need for serial testing.
Background
Reverse-transcriptase PCR tests are the most widely used type of NAATs used by clinicians to detect SARS-CoV-2 in respiratory tract specimens. A variety of gene targets are available across different assays, including the envelope gene, the nucleocapsid gene, the ORF1ab gene and the spike gene. Most assays are designed to detect two or more gene targets to reduce the likelihood of a false positive. FDA maintains an up-to-date list of molecular COVID-19 tests with emergency use authorization.
Guidelines
IDSA guidelines recommend NAAT testing for various scenarios, including in all symptomatic individuals suspected of having COVID-19; in asymptomatic individuals with known or suspected exposure; and in asymptomatic individuals when the results will impact isolation/quarantine/personal protective equipment usage decisions. Repeat testing is recommended in symptomatic individuals with intermediate or high clinical suspicion if the initial test result is negative.
NIH COVID-19 guidelines recommend using either a NAAT or an antigen test to diagnose acute SARS-CoV-2 infection and specify that NAAT is “considered the gold standard for detecting current SARS-CoV-2 infection.”