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Molecular diagnosis of severe acute respiratory syndrome virus 2 (SARS-CoV-2) Covid-19: State of the art and where we go from here

James B. Mahony

Department of Pathology & Molecular Medicine, McMaster University, and The Research Institute of St. Joe’s Hamilton, St. Joseph’s Healthcare Hamilton, Hamilton, Ontario Canada


There are a large number of PCR tests available from a variety of manufacturers that have received EUA by the FDA. These PCR tests together with research-based tests have been used to quantitate viral RNA during the course of infection in a variety of Covid-19 patients. The most commonly used molecular test for diagnosing SARSCoV- 2 has been the RT-qPCR test. None of the molecular tests including RT-qPCR, LAMP, CRISPR or NGS however, can distinguish between live and dead virus and provide this important piece of information to public health authorities to help control the pandemic. Similarly, detection of viral antigens or antibodies do not provide information on infectivity which is important for people returning to the workplace after quarantine. Some newly developed saliva tests including the BinaxNOW rapid COVID-19 test (Abbott Diagnostics) for nasal swabs from symptomatic individuals up to 7 days post onset of symptoms utilize lateral flow of lateral flow technology to provide rapid easy to read test results in under 30 minutes and should help to increase testing volumes. Saliva antigen tests that measure viral proteins represent the first POC tests that do not require laboratories to perform the testing and can be performed by non-healthcare workers. The advantage of saliva antigen tests is that they can be self-administered and used at home or in a variety of settings including the workplace. Saliva RNA testing on the other hand, usually requires a laboratory to perform RNA extraction and nucleic acid amplification and therefore do not provide rapid resulting. The next major and long-awaited development in Covid-19 diagnostics will be the development of an RNA POCT providing a rapid result that can be performed at the point-of-need without the need for any instrumentation or equipment. A rapid POCT for viral RNA will provide additional information on infectivity beyond what the antigen test provides and may replace the antigen POCT for determining whether a person is infectious.

RT-PCR; RT-LAMP; NGS; point-of-care (POC) testing
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