Coronaviruses are a family of viruses pathogenic to humans. Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), a single-stranded, positive-sense RNA virus. The virus can be translated directly into protein, and the synthesized negative RNA strand serves as a template for viral replication. The SARS-CoV2 genome encodes for structural proteins (spike, membrane, envelope, nucleocapsid) and regions necessary for viral replication (the open-reading frame 1a or 1b, RNA-dependent RNA polymerase, hemagglutinin-esterase). Laboratory diagnostics typically target 2 distinct genetic regions in the development of their assays to improve test accuracy and to reduce false-positive results through cross-reactivity with other Coronaviridae.
Most commonly, the diagnosis is made using a nasopharyngeal swab, but nasal swabs and saliva samples are becoming more common. Samples are preserved and transported in a viral stabilizing medium. The major laboratory-based methods currently available for the detection of SARS-CoV2 include real-time reverse-transcription polymerase chain reaction (RT-PCR), loop or isothermal nucleic acid amplification testing, next-generation sequencing, antigen-based testing, and clustered regularly interspaced short palindromic repeat–based technologies. RT-PCR is the most widely used technique for diagnosis of COVID-19. It is a specialized, quantitative molecular technique available in most major laboratories and the current gold standard for SARS-CoV2 infection diagnosis. RT-PCR involves 2 major steps: viral extraction and amplification. Initially, no SARS-CoV2–specific primers existed.
Reference link- https://www.ahajournals.org/doi/10.1161/CIRCULATIONAHA.120.051183