Why CDC Withdrew Its Original PCR Test for COVID

The agency moved to a newer test model that can determine whether you have COVID or another virus.

In December 2021, the Centers for Disease Control and Prevention (CDC) discontinued a test it designed to look for SARS-CoV-2 (the virus that causes COVID-19).

The test, officially called CDC 2019-nCoV Real-Time RT-PCR Diagnostic Panel, was the first COVID test to receive emergency use authorization (EUA) from the Food & Drug Administration (FDA) in the early days of the pandemic.

But with tens of thousands of new cases each day (per the CDC), the need for testing certainly hasn't gone away. So why did the CDC retire it?

The CDC's rationale is pretty straightforward. Here's why the CDC's taking back its EUA request for this particular COVID test at the end of 2021.

CDC's PCR test , Midsection of female doctor with swab test sample during COVID-19 crisis. Female medical professional is holding test tube in hospital. She is wearing protective suit. , Doctor/Nurse with Swab Test Sample in Hospital, PCR Device
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Why the CDC Will No Longer Use Its Original COVID Test

According to the CDC, the agency decided to stop using its original polymerase chain reaction (PCR) test for SARS-CoV-2 because there was a newer, more resource-efficient model to replace it.

The CDC encouraged labs to switch to a test called the Flu SC2 Multiplex Assay, a single test that can generate results for SARS-CoV-2, influenza A, and influenza B at the same time.

The announcement on its website reads, "Although the CDC 2019-nCoV Real-Time RT-PCR Diagnostic Panel filled an important unmet need when it was first developed and deployed, the demand for this test has declined with the authorization of higher-throughput alternatives and multiplexed assays that detect both SARS-CoV-2 and other common respiratory pathogens simultaneously."

The US Food and Drug Administration (FDA) granted Emergency Use Authorization (EUA) for the Flu SC2 Multiplex Assay test on July 2, 2020.

"The CDC has recognized that it would become increasingly important to test for both COVID and other viruses, like influenza and RSV [respiratory syncytial virus] as we move into the fall and winter," said Matthew Binnicker, PhD, director of clinical virology in Mayo Clinic's Division of Clinical Microbiology.

The main difference between the two tests is that the CDC's original test, the CDC 2019-nCoV Real-Time RT-PCR Diagnostic Panel, was only looking for SARS-CoV-2 and ignoring genetic material from other viruses entirely. It couldn't tell a lab whether your sample contained any viral material, just whether it had genetic material from the COVID coronavirus.

"When you develop and submit a new test for authorization from the FDA, you have to show that you checked the specific genetic sequence you're testing for against similar and related organisms, and that there's no cross-reactivity. Your test has to be specific for that organism you're trying to measure," said Dwayne Breining, MD, executive director and medical director of Northwell Health Laboratories.

"There's a reason why the people who developed this type of testing won a Nobel prize back in the day. PCR tests are among the most accurate clinical tests that have ever been developed."

Bottom line: The CDC's original PCR test for COVID isn't going away because of inaccurate results—it's just that there are more comprehensive tests available that can help doctors figure out whether you have COVID, the flu, or some other bug, and give you the right treatment. Taking this test "off the market" helps push labs to adopt those other tests that can check for multiple viruses.

Tons of New COVID Tests Available

Experts say that, while not explicitly mentioned in the announcement, there is another big reason behind the CDC's latest move. It has to do with the sheer number of tests that have received EUA since the CDC's PCR test first debuted in February 2020, when there was a huge need for testing and no other options in the US.

The CDC, as a federal agency, was uniquely positioned to rapidly create an effective test and deploy it to government-run labs across the country.

"The CDC does this in special circumstances for new and emerging pathogens, like COVID. They had also done a similar thing for Ebola and the Zika virus," said Dr. Breining.

But since then, over 250 molecular diagnostic tests have been approved by the FDA, according to its database. And while they often rely on the same PCR technology used in the CDC's first test, many of the newer tests are much more efficient for labs to process, allowing them to conduct far more testing on a daily basis without compromising accuracy.

"The CDC is not really in the testing business per se," said Dr. Breining. The CDC rolled out the first test quickly to jumpstart the country's ability to test for SARS-CoV-2, said Dr. Breining. That paved the way for other groups, like private companies and nonprofit organizations, to develop new COVID-19 tests.

"Once the industry is on its feet, the CDC typically backs away from the situation so they can move onto the next thing," said Dr. Breining. "That pattern of the CDC developing the testing then backing away is typical."

What Does This Mean For You?

The CDC's move shouldn't have caused any issues for people who needed a COVID test. For one, it only withdrew its EUA request for its own test. This will not impact the hundreds of other tests still in use.

Plus, very few labs in the country were still using this test, said Dr. Breining. The CDC has only been providing its original PCR test for COVID to certain public health laboratories run by the government—not hospitals or commercial laboratories where many COVID tests are processed. Those laboratories had until the end of the year to switch to another option, such as the CDC's "multiplex assay," which tests for COVID and multiple flu strains, per the agency's announcement.

"Almost every laboratory moved beyond the CDC COVID testing assay many months ago. If a person did happen to use a lab that used the CDC assay, that lab would have switched over to another test and it will be seamless for the person who gets testing done," said Dr. Breining.

What's more, moving toward comprehensive testing for multiple viruses at the same time can offer major benefits to both individuals and public health. Knowing which type of infection a patient has gives doctors the opportunity to prescribe the right treatment early on, said Dr. Binnicker.

It will also provide officials with more data on clusters of COVID, the flu, and other infections, so they can "save time and resources" during flu season, the CDC points out. So the new test is a better public health option than the original.

"Any time an organization or company or government agency takes something away, there's always going to be questions, and people are going to fill that empty space with misinformation and rumors about what happened," said Dr. Binnicker.

"But the consensus in the laboratory testing community and healthcare community is that the CDC implemented their test during the early stages of the pandemic to respond to an unmet need, and now that need has been met by more than 200 different diagnostic tests that, in some cases, are faster and sometimes provide physicians with more information."

The information in this story is accurate as of press time. However, as the situation surrounding COVID-19 continues to evolve, it's possible that some data have changed since publication. While Health is trying to keep our stories as up-to-date as possible, we also encourage readers to stay informed on news and recommendations for their own communities by using the CDC, WHO, and their local public health department as resources.

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