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Response to COVID-19 hinges on a test—but it’s not the kind your doctor performs

Forget about cultures or x-rays—for this virus, you need PCR

The virus that causes COVID-19 hails from the same family of viruses that lead to MERS and SARS. The US CDC recently released the COVID-19 real-time RT-PCR Diagnostic Panel for use on patients who meet the agency’s testing criteria. The test includes probes, primers, and positive controls.

The coronavirus, which was first identified in China in the final days of 2019, is by no means the first coronavirus to spark worldwide concern. The virus, initially known as 2019-nCoV* but now officially called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is merely the latest in a long line of viruses known among those in the medical and scientific community as 229E, NL63, OC43, and HKU1.

Novel coronavirus causes a respiratory illness with symptoms ranging from a mild cough to pneumonia, including fever, flu-like symptoms, and shortness of breath. Severe cases can lead to organ failure, and antibiotics are of no use.

There’s only one way to know if you have SARS-CoV-2 and not some other virus, and that is by confirming the presence of its viral genome sequence.

The coronavirus family includes SARS, pneumonia, and even the common cold

Coronaviruses are a sprawling family of pathogens, including everything from the common cold to MERS. It got its name because of how it looks under a microscope—there are crown-like spikes protruding from the surface of the virus, which affects how it binds to the host cell and infects it. Tests show that the virus causing coronavirus disease 2019 (COVID-19) shares 80% of its genetic code with another infamous coronavirus, SARS.

With the virus spreading, the US Food and Drug Administration issued an Emergency Use Authorization (EUA) on February 4, 2020 for the Centers for Disease Control and Prevention (CDC) to distribute virus test kits.

“This continues to be an evolving situation and the ability to distribute this diagnostic test to qualified labs is a critical step forward in protecting the public health,” said FDA Commissioner Stephen M Hahn, MD, in an FDA press release. “Our collaboration with the CDC has been vital to rapidly developing and facilitating access to this diagnostic test.”

Under that EUA, the use of the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time Reverse Transcriptase (RT)-PCR Diagnostic Panel is approved for patients who meet CDC testing criteria

CDC tests include probes, primers, and positive controls

COVID-19 diagnostic testing can be conducted at the CDC and public health labs, though in the US, at least, any test which comes back positive must be sent to the CDC for confirmatory testing. According to the CDC, each lab that places an order will initially receive one panel, with each panel able to test 700 to 800 patient specimens. The CDC 2019-nCoV Real-Time RT-PCR Diagnostic Panel contains:

  • 2019-nCoV_N1, 2019-nCoV_N2 and 2019-nCoV_N3 primers and probes that target the nucleocapsid (N) gene and are designed for both universal detection of SARS-like coronavirus as well as specific detection of the COVID-19 virus
  • RP primers and probes that target the human RNase P gene

The test also requires a human specimen control (HSC) and a positive control (nCoVPC), ordered separately, as well as a no-template control (NTC).

The RT-PCR test detects the virus from respiratory secretions like nasal or oral swabs, although the CDC has warned that negative results don’t necessarily rule out an infection—the test should be used as a tool alongside clinical observations, patient history, and epidemiological information. On February 4, 2020, the CDC released a 12-page instruction booklet for the test, and has also released a detailed set of instructions, including standards for test interpretation. The agency has also published the sequence for each primer and probe.

The test shipped by the CDC on February 6, 2020, the agency said, is designed for use with the existing test instruments frequently used to verify seasonal influenza. Results can be ready within 4 hours.

Private companies lend a hand with tests of their own

Meanwhile, a number of companies have jumped in with their own tests.

Clinical diagnostics company Novacyt’s molecular diagnostics division Primerdesign launched a molecular research use only test at the end of January. Primerdesign’s coronavirus test is capable of detecting only the 2019 strain of the virus. It is stable at ambient temperatures, eliminating the need for refrigerated shipping to tropical climates.

Finnish company Mobidiag has initiated the development of a Novodiag molecular diagnostic test to enable swift diagnosis of COVID-19. Chinese clinical diagnostics company Autobio Diagnostics and Automobi Molecular Diagnostics, a joint venture firm of Mobidiag and Autobio, are also part of the project. Novodiag’s assay will leverage a fully automated “sample-in, result-out” system to identify the viruses simultaneously in around 30 minutes.

On February 10, 2020, California-based diagnostics firm Cepheid announced the development of an automated coronavirus molecular test which will also deliver results in about a half hour. Cepheid’s test is meant to address problems with early nucleic acid tests (NATs), which produced large numbers of false negatives.

"At the moment, more and more cases in Wuhan are flaring up collectively in family groups, and the majority are of the concealed onset type," Dr Zhang Xiaochun, a deputy director of the medical imaging department at Zhongnan Hospital of Wuhan University, told Caixan Global, as reported in the Singapore Straits Times. "They may have undergone one or even several NATs and shown no clinical symptoms, but keeping them under observation at home is bound to spread the disease further."

Once finalized, according to Medical Device Network, Cepheid plans to ask the FDA for authorization to deliver the assay globally.

* Testing product names were based off the initial 2019-nCoV title. Currently, SARS-CoV-2 refers to the virus which causes COVID-19. Original titles of the testing products will not change, so please note these distinctions to avoid confusion in the terminology.

Published Mar 14, 2020