Story Twists Facts on Diagnosing Breakthrough COVID-19 Cases


SciCheck Digest

A viral headline shared on social media falsely asserts that the Centers for Disease Control and Prevention changed testing thresholds to “virtually eliminate” COVID-19 cases among vaccinated individuals. That’s wrong. The threshold in question simply applies to whether or not there is enough virus present in a sample for further analysis.

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As part of its efforts to track breakthrough COVID-19 cases, the Centers for Disease Control and Prevention recently offered public health departments and labs guidance for when to send the federal agency samples from such cases.

The agency defines breakthrough infections as those that occur when someone tests positive for SARS-CoV-2, the virus that causes COVID-19, at least two weeks after they receive their final dose of a vaccine. Specimens from some of those cases are collected so that scientists can sequence the sample, which can identify specific variants of the virus.

A false claim spreading on social media distorts the facts on this issue, wrongly asserting that the CDC has changed COVID-19 testing procedures to no longer count cases among vaccinated people.

The website Zero Hedge — known for spreading misinformation — ran a May 23 story headlined, “Caught Red-Handed: CDC Changes Test Thresholds To Virtually Eliminate New COVID Cases Among Vaxx’d.” It was shared on Facebook more than 13,000 times, according to CrowdTangle analytics data.

The story was actually republished from a website called, whose own post garnered more than 2,000 shares on Facebook.

But the claims made in the story rest on a misrepresentation of what the CDC said.

The piece begins by accusing the agency of “altering its practices of data logging and testing for ‘Covid19’ in order to make it seem the experimental gene-therapy ‘vaccines’ are effective at preventing the alleged disease.”

First of all, as we’ve explained, experts say the COVID-19 vaccines authorized for emergency use in the U.S. are not gene therapy. While some have made that claim about the mRNA vaccines — from Pfizer/BioNTech and Moderna — the vaccines do not modify a person’s genes. A Food and Drug Administration spokesperson also told us in a recent email that “none of these vaccines are defined as a gene therapy.”

And the vaccines have proven to be highly effective in clinical trials — and, so far, in real-world use. For more, see our SciCheck stories on the Pfizer/BioNTech, Moderna and Johnson & Johnson COVID-19 vaccines.

The viral story focuses on polymerase chain reaction, or PCR, tests — which have been used to diagnose COVID-19 — and the issue of cycle threshold values. The piece dubiously purports that high cycle threshold values have been responsible for false-positive cases that have helped to cause “an entirely created pandemic narrative.”

As we’ve outlined before, a PCR test works by scanning the RNA in a sample, such as a nose swab, and searching for the virus RNA. The test analyzes samples by amplifying a segment of the virus’s genetic material in a series of cycles. A sample with a higher viral load — meaning more virus is present in the sample — will require fewer cycles to detect the novel coronavirus. Lower viral loads will be detected at higher cycles.

There is no universal threshold setting or endpoint — “although 40-45 cycles is often used as the endpoint” of a PCR run — Ian Mackay, a virologist in Australia, previously told us.

The central debate among scientists in regards to COVID-19 cases detected at high cycle threshold values (meaning less virus is present) isn’t whether they are false positives, but how to interpret and act on those cases. For example, a sample detected at a cycle threshold of 45 could mean the person already had COVID-19 and is no longer contagious; though, alternatively, it could also mean someone only recently became infected.

The viral story claims that “NOW, and only for fully vaccinated people, the CDC will only accept samples achieved from 28 cycles or fewer. That can only be a deliberate decision in order to decrease the number of ‘breakthrough infections’ being officially recorded.”

That’s not what the CDC has said about a cycle threshold of 28.

Instead, the CDC said samples submitted for genetic sequencing would need to be at that threshold. Scientists use sequencing to decode the genes of the virus to better understand factors such as its spread and evolution.

On its informational page for public health departments and laboratories, the CDC provides instructions for submitting samples to the agency for breakthrough infection monitoring. There, the CDC says: “For cases with a known RT-PCR cycle threshold (Ct) value, submit only specimens with Ct value ≤28 to CDC for sequencing. (Sequencing is not feasible with higher Ct values.)”

The threshold doesn’t pertain to deciding whether the test is positive or not.

“The CDC is still counting positive SARS-CoV-2 molecular results with any cycle threshold value as it pertains to case counts,” Matthew Binnicker, a professor of laboratory medicine and pathology at the Mayo Clinic, told us in an email. “However, for sequencing studies, laboratories need a certain amount of the virus’ RNA in a sample for the sequencing to be successful. In other words, if there is a low amount of the viral RNA present, the sequencing will not produce results that can be interpreted.”

CDC spokeswoman Jasmine Reed told us the same.

Reed said in an email that the “Ct value ≤28 is not used to define whether a specimen is positive or negative for SARS-CoV-2. The Ct value cutoff of 28 is only for submitting specimens that test positive for SARS-CoV-2 to CDC for sequencing.”

“Different labs will use different cutoffs for deciding when to perform sequencing. However, the Ct value needed to perform sequencing will not vary by vaccination status,” she added. “In general, CDC uses the same Ct value cutoff for submitting other SARS-CoV-2 surveillance specimens for sequencing. That cutoff is set because at Ct values >28 it becomes increasingly difficult to successfully sequence the specimen because the RNA levels in the specimens are generally too low.”

All Positive COVID-19 Cases Are Counted

The viral story goes on to wrongly say that “being asymptomatic – or having only minor symptoms – will no longer count as a ‘Covid case’” if the person is vaccinated, even if someone tests positive.

The story cites a CDC May 1 update that says the agency “transitioned from monitoring all reported vaccine breakthrough cases to focus on identifying and investigating only hospitalized or fatal cases due to any cause.”

It’s true that the CDC has decided to no longer investigate and report on all breakthrough cases. Instead, it will actively investigate and report on hospitalized or fatal cases, Reed told us. The CDC developed a national database through which state health departments can enter and manage data for such cases.

“As of May 1, 2021 CDC has transitioned from public reporting of all vaccine breakthrough cases to focus on identifying and actively investigating hospitalized or fatal cases for clustering by patient demographics, geographic location, time since vaccination, vaccine type, and SARS-CoV-2 lineage,” Reed said. “Some health departments may continue to report all vaccine breakthrough cases; however, CDC will focus its public reporting on hospitalized and fatal cases.”

The CDC page on breakthrough infection reporting notes: “Data on patients with vaccine breakthrough infection who were hospitalized or died will be updated regularly.” It adds that studies around the country are also being conducted on breakthrough infections, regardless of clinical status, “to supplement the national surveillance.”

But the May 1 change does not mean that positive COVID-19 tests among vaccinated people will “no longer be recorded” as COVID-19 cases, as the story claims.

If someone tests positive for COVID-19, “you are going to be recorded as a case, there is no way around it,” Ali Mokdad, chief strategy officer for population health at the University of Washington, told us in a phone interview. “They didn’t change the rules.”

In other words, if someone who is vaccinated tests positive for COVID-19, that case will still be reported in standard COVID-19 case counts. Jade Fulce, another CDC spokeswoman, confirmed that “breakthrough cases are captured in the regular case reporting system.”

That said, Mokdad — who previously worked at the CDC — is among some critics of the agency’s decision to focus only on breakthrough infections that result in hospitalizations or deaths.

By not more closely investigating all breakthrough infections, Mokdad argues, opportunities are missed to more closely understand trends in breakthrough infections — such as the role of specific variants, or whether the infections are occurring following a specific vaccine, in a certain time period or in certain demographics.

He argues that the CDC should conduct regular random sampling among vaccinated people — especially since most asymptomatic breakthrough infections will not be tested and identified — to observe how things change over time and in different populations.

The CDC in a May 25 report said there were 10,262 breakthrough infections reported between Jan. 1 and April 30. About 101 million people were fully vaccinated by April 30.

While that suggests such cases are rare, the agency acknowledged that “the number of reported COVID-19 vaccine breakthrough cases is likely a substantial undercount of all SARS-CoV-2 infections among fully vaccinated persons.” That’s in part because the data may not be complete and because people with such infections, “especially those who are asymptomatic or who experience mild illness, might not seek testing.”

Editor’s note: SciCheck’s COVID-19/Vaccination Project is made possible by a grant from the Robert Wood Johnson Foundation. The foundation has no control over our editorial decisions, and the views expressed in our articles do not necessarily reflect the views of the foundation. The goal of the project is to increase exposure to accurate information about COVID-19 and vaccines, while decreasing the impact of misinformation.


Binnicker, Matthew. Professor of laboratory medicine and pathology, Mayo Clinic. Email to 24 May 2021.

Caryn Rabin, Roni. “C.D.C. Will Not Investigate Mild Infections in Vaccinated Americans.” New York Times. 25 May 2021.

COVID-19 Vaccine Breakthrough Case Investigation and Reporting.” Centers for Disease Control and Prevention. Accessed 25 May 2021.

COVID-19 Vaccine Breakthrough Infections Reported to CDC — United States, January 1–April 30, 2021.” Morbidity and Mortality Weekly Report. Centers for Disease Control and Prevention. 25 May 2021.

Fichera, Angelo. “Texas Doctor Spreads False Claims About COVID-19 Vaccines.” 26 Mar 2021.

Fichera, Angelo. “Viral Posts Distort WHO Guidance on COVID-19 Tests.” 29 Jan 2021.

Food and Drug Administration. Email to 12 Apr 2021.

Genomic Surveillance for SARS-CoV-2 Variants.” Centers for Disease Control and Prevention. Updated 17 May 2021.

McDonald, Jessica. “The Facts on Coronavirus Testing.” 10 Mar 2020.

Fulce, Jade. Spokeswoman, Centers for Disease Control and Prevention. Email to 27 May 2021.

Mokdad, Ali. Chief strategy officer for population health, University of Washington. Phone interview with 26 May 2021.

Published SARS-CoV-2 Sequences.” Centers for Disease Control and Prevention. Accessed 27 May 2021.

Reed, Jasmine. Spokeswoman, Centers for Disease Control and Prevention. Email to 24 May 2021.

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