Why CDC Withdrew Its Original PCR Test for COVID-19

As we all know, getting tested for COVID-19 if you think you have symptoms or have been exposed to someone who has COVID-19 is essential to help stop the spread of SARS-CoV-2 (the virus that causes COVID-19). Diagnostic tests can show if you currently are infected with SARS-CoV-2.

There are two types of COVID-19 diagnostic tests, molecular and antigen:

• Molecular tests include polymerase chain reaction (PCR) tests.
• Antigen tests are often called rapid tests. Most authorized at-home over-the-counter COVID-19 tests are antigen tests.

The original PCR diagnostic test used to detect SARS-CoV-2 was developed by the Centers for Disease Control and Prevention (CDC) in the early stages of the pandemic. But in July 2021, CDC announced it was discontinuing that test by the end of the year.

The test was officially called CDC 2019-nCoV Real-Time RT-PCR Diagnostic Panel. It was the first COVID-19 test to receive emergency use authorization (EUA) from the Food and Drug Administration (FDA) in the early days of the pandemic.

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

CDC's rationale is pretty straightforward. Here's why CDC took back its EUA request for this particular COVID-19 test at the end of 2021.

Why CDC No Longer Uses Its Original COVID-19 Test

CDC 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. Laboratories had until the end of 2021 to switch from using the original test.

CDC encouraged labs to switch to a test called the Flu SC2 Multiplex Assay. The Flu SC2 Multiplex Assay is a single test that can generate results for SARS-CoV-2, influenza A, and influenza B at the same time, says CDC. Having a combined test for influenza and COVID-19 saves everyone time because now you only need one test instead of two when you come in with symptoms of either disease.

The FDA granted EUA for the Flu SC2 Multiplex Assay test on July 2, 2020. Basically, this type of authorization is given only to medical products used to diagnose, treat, or prevent conditions that are needed during a public health emergency. These products haven't been through years of testing like other products on the market.

"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," Matthew Binnicker, PhD, director of clinical virology in Mayo Clinic's Division of Clinical Microbiology, told Health.

The main difference between the two tests is that CDC's original test, 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 material from other viruses, but it could tell whether the sample had genetic material from SARS-CoV-2.

"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," Dwayne Breining, MD, executive director and medical director of Northwell Health Laboratories, told Health.

"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," said Dr. Breining.

Bottom line: CDC's original PCR test for COVID-19 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-19, 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 at the same time.

Tons of New COVID-19 Tests Available

Experts say that, while not explicitly mentioned in the announcement, there is another big reason behind CDC's latest move. It has to do with the sheer number of tests that have received EUA since CDC's PCR test first debuted in February 2020, when there was a huge need for testing and a lack of other options in the United States.

As a federal agency, CDC 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," said Dr. Breining, referring to SARS-CoV-2. "They had also done a similar thing for Ebola and the Zika virus."

But since then, over 250 molecular diagnostic tests for SARS-CoV-2 have been authorized by the FDA. And while they often rely on the same PCR technology used in 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. CDC rolled out the first test quickly to jumpstart the country's ability to test for SARS-CoV-2, explained 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?

CDC's move shouldn't have caused any issues for people who needed a COVID-19 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. CDC has only been providing its original PCR test for COVID-19 to certain public health laboratories run by the government—not hospitals or commercial laboratories where many COVID-19 tests are processed.

"Almost every laboratory moved beyond the CDC COVID-19 testing assay. 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 Binnicker.

It will also provide officials with more data on clusters of COVID-19, the flu, and other infections, so they can "save both time and resources" during flu season, 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 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," said Dr. Binnicker.

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.