About COVID-19 Nucleic Acid Testing

The majority of molecular-based detection kits made available for SARS-CoV-2 are real-time reverse transcriptase PCR assays. In some of the kits that were released in the early days of the outbreak, mismatching with SARS-CoV was a problem. But as time went on and more countries became involved, more companies began developing highly specific test kits for SARS-CoV-2.  These kits were helped by the public database GISAID  , which laboratories were using to share sequence information from positive SARS-CoV-2 samples to the science community.

Many of the kits contain three assays, each assay targeting a different gene in the virus, so if the virus does mutate the chances of all three targets mutating is low. However if one, or two, of these assays, is positive, then the result must be recorded as inconclusive. These targets are the Orf1 gene (human RNA polymerase protein), the N-gene (the nucleocapsid protein) and the E-gene (envelope protein). There are some kits which target the S-gene (spike protein) but these are limited. An increasing number of the products have received Emergency Use Authorisation (EUA) from the FDA and have received CE-marking for sale in Europe, with still some products only available for Research Use Only (RUO).

Swabs: Based on CDC guidelines for clinical specimens  , swabs with synthetic fibers and plastic shafts should be used for nasopharyngeal collections when 2019-nCoV is suspected. It's important not to use calcium alginate swabs or those with wooden shafts as they may contain materials that interfere with test results. For upper respiratory specimens, the CDC is recommending nasopharyngeal washes/aspirates, nasal aspirates or to collect both a nasopharyngeal swab AND an oropharyngeal swab made of synthetic fibre with plastic applicators. Once the specimens are collected, it is recommended that the swabs are placed in 2-3 ml of viral transport media. Suppliers of these swabs are listed in tables below.