Horse Gulch Blog

Watchdogging for the greater Durango area

20 Dec 2020

PCR tests eligible for add-on recompense if results are positive for COVID-19

Posted by Adam Howell


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PCR tests that are found positive for COVID-19 are eligible for an add-on reimbursement from Medicare that’s higher than the payment for negative results. This, suggesting the existence of a possibly undisclosed conflict of interest for participating laboratories.

PCR tests“To address potential Medicare program integrity risks, effective with admissions occurring on or after September 1, 2020, claims eligible for the 20 percent increase in the MS-DRG weighting factor will also be required to have a positive COVID-19 laboratory test documented in the patient’s medical record. Positive tests must be demonstrated using only the results of viral testing (i.e., molecular or antigen), consistent with CDC guidelines. The test may be performed either during the hospital admission or prior to the hospital admission,” according to a Medicare Learning Network document from the Centers for Medicare and Medicaid Services.

“Under President Trump’s leadership, the Centers for Medicare & Medicaid Services (CMS) today announced new actions to pay for expedited coronavirus disease 2019 (COVID-19) test results. CMS previously took action in April 2020 by increasing the Medicare payment to laboratories for high throughput COVID-19 diagnostic tests from approximately $51 to $100 per test. Today, CMS is announcing that starting January 1, 2021, Medicare will pay $100 only to laboratories that complete high throughput COVID-19 diagnostic tests within two calendar days of the specimen being collected. Also effective January 1, 2021, for laboratories that take longer than two days to complete these tests, Medicare will pay a rate of $75.,” according to a press release from the Centers for Medicare and Medicaid Services.

More specifically, the Medicare Hospital Inpatient Prospective Payment System Add-On Payment For COVID-19 Patients During Emergency Period is described on page 142 in Section 3710 of the ‘‘Coronavirus Aid, Relief, and Economic Security Act’’ or the ‘‘CARES Act.”

Representatives from labs that analyze most of the samples from Durango that are tested for COVID-19 refused to comment for this story. A FOIA request for records of the reimbursements to labs servicing Durango from the Centers for Medicare and Medicaid Services was submitted on December 14, 2020.

Possible violation of guideline integrity for those administering PCR tests

Multiple individuals who were tested through Cedar Diagnostics or San Juan Basin Health Department were not informed before taking the test that a positive test result might bring in higher reimbursement than a negative one for those administering or analyzing the test.

For UniPath, the lab that analyzes samples that were collected by Cedar Diagnostics, their testing could influence or be perceived as influencing guideline decisions.

As a member of the College of American Pathologists, UniPath appears to follow evidence-based guideline principles in an attempt to manage conflicts of interest. In writing, these evidence-based guideline principles are outlined in a document on the organization’s website under the heading “Management of Conflict of Interest.”

“We uphold guideline integrity by avoiding or actively managing conflict of interest, real or perceived, which could influence or be perceived as influencing guideline decisions,” the CAP Guideline Principle states. “Panel members are often leaders within their field and may have associations with industry. We strive to balance the panel with knowledgeable subject matter members while ensuring that majority of the panel is free from conflicts of interest. Disclosure is required throughout the guideline process, shared with all panel members, and cited in the manuscript.”




UniPath Lab director obfuscates ability of PCR tests in determining COVID-19 infection

Differentiating between what is or is not an active COVID-19 infection with a PCR test was not something I could get a straight answer on from the director of UniPath Lab, the lab that processes samples that are collected by Cedar Diagnostics in Durango.

Jonathan Mancini, the Director of Operations for UniPath Lab in Denver, talked to me extensively about PCR tests that are done at their lab, but he did not provide me with any definitions for ‘active infection’ or an ‘inactive infection’.

Me: The virus is present with a positive test result for COVID-19 at your lab. But it could be just dead virus at that point. And it could’ve been 3 months since the virus was actually active or live in the patient who was tested.

Mancini: “Could the virus be dead? Technically, yes,” said Mancini. “But, the time frame. I don’t think there’s any research to show that the virus could still be in the body for three months. A couple of days, maybe a week, I could see, but again, I’m not that well versed in virology to say that. That’s something that you would have to wade from a publication from the CDC or something like that. Because most of the time after an infection has cleared, the RNA DNA could linger for a short amount of time. But I would hesitate to say that amount of time.”

Does positive PCR test for COVID-19 RNA indicate presence of an active virus? We may never know

Me: So a positive test result from your lab could indicate the presence of all dead RNA. Is that not true?

Mancini: “It does take a certain amount of time for the virus to shed that RNA,” said Mancini. “So whether it’s still an active infection–and I hesitate using that word active infection–but whether the virus is still active in the body or not, that’s not something that our tests can determine. Our tests again can just determine that there is COVID-19 RNA in the sample.”

“But if COVID-19 in the sample is present. Whether it’s an infection that was kicked a week ago, or whether it’s an active infection, it’s relatively recent in the body. The virus is still present,” Mancini said.

“It’s just a diagnostic test that says that the sample we received does contain COVID-19 virus,” said Mancini. “But that is all we can tell the provider.”

“We cannot differentiate. The only thing we can say is this sample contains the nucleic acid that is part of the COVID-19 virus,” Mancini said.

“When you say infection, an infection is really if you have the virus,” said Mancini. “How the virus reacts to or how your body reacts to the virus and things like that, I can’t say anything. The only thing I can say is from our test is the swab submitted either has COVID or it does not have COVID.”

PCR tests indicate presence of nucleic acids, not infectious virus, says virologist

In contrast to literature from the U.S. FDA, and Cedar Diagnostics LLC that says a positive COVID-19 PCR test means that an active infection is present, is the claim from a Columbia University professor who states the opposite.

Vincent R. Racaniello, a Higgins Professor in the Department of Microbiology and Immunology at Columbia University’s College of Physicians and Surgeons, wrote in Virology Blog about PCR testing.

In a Virology Blog article about a study of the sexual transmission of Zika virus among mice, Racaniello said that a PCR test does not indicate the presence of infectious virus. Instead, what a positive test indicates is the presence of nucleic acids and viral RNA, he said.

Specifically, the Zika study demonstrated that viral nucleic acid detected by polymerase chain reaction (PCR) is not the same as infectious virus, Racaniello said.

Racaniello did not reply to my request for an interview for this story.

UniPath, Cedar Diagnostics and U.S. FDA claims about capability of PCR tests disputed by acclaimed virologist

Alarmingly, the online literature from both the U.S. Food and Drug Administration and Cedar Diagnostics inaccurately claims that a PCR test diagnoses the presence of an active infection. According to Racaniello’s research, those claims about PCR testing are false.

“A diagnostic test can show if you have an active coronavirus infection and should take steps to quarantine or isolate yourself from others,” says an FDA post on Coronavirus Disease 2019 Testing Basics. “Currently there are two types of diagnostic tests– molecular tests, such as RT-PCR tests, that detect the virus’s genetic material, and antigen tests that detect specific proteins from the virus. Public health professionals may be interested in the article A Closer Look at COVID-19 Diagnostic Testing.”

PCR tests

A screenshot from an FDA post about PCR testing.

Similar to the FDA, is wording from Cedar Diagnostics in a document about the SARS CoV-2 screening test on their web page about COVID-19. The PDF document contains a number of frequently asked questions from patients about the novel coronavirus (COVID-19).

What does a positive COVID-19 PCR test mean?

A positive test is confirmatory of active COVID-19 infection and warrants appropriate action, including quarantine of you and your contacts, as well reporting to the county health department,” says the Cedar Diagnostics document.

PCR tests look for nucleic acids, not active infections

How the PCR test analysis methodology occurs at UniPath Lab

Determining whether a PCR test sample is positive for COVID-19 requires a continuous cyclical process that tests for three RNA genes, according to Mancini.

“When we receive a sample, typically they’re nasopharyngeal, sometimes orophoryngeal swabs. So those swabs, the whole purpose of it is to obtain a good collection so that we can say yes the sample has COVID, or no it doesn’t. When the swab is received in the laboratory, the process is to put the swab in the media that we receive in that swab into an extraction procedure.

That extraction procedure splices the cells, pulls out the RNA and DNA and kind of throws away everything else. All the proteins, all the kind of cellular junk. We keep just the nucleic acids. That nucleic acid is combined with a TaqPath mixture that has sequences–DNA RNA sequences–that are specific to COVID-19.

If it finds those sequences once we put it on our PCR instrument that heats and cools for 40 cycles, what will happen is those sequences coupled with other enzymes will amplify the RNA or DNA of interest. That RNA or DNA of interest, once it starts amplifying, it breaks apart the fluorescent dye and actually fluoresces. That fluorescent is measured on every cycle threshold. And when the amplification starts logarithmically amplifying, that’s when we can say this RNA DNA is present in the sample. Therefore this patient’s sample is positive for COVID-19,” said Mancini.


How PCR tests amplification works at UniPath Lab

“They are all ran at 40, but when it starts amplifying, you will have that numeric value, and you will be able to see that this became positive at cycle 25. But everything is ran at 40 cycles,” said Mancini.

“Looking at each individual patient sample, you are able to determine that it is positive and at what threshold cycle it became positive,” he said.

Me: Are there some samples that become positive at 40 amplifications?

“It’s possible, but in our laboratory, I can say we’ve never seen anything that low,” said Mancini.

“We have a rule here in the laboratory that when amplification is past 30 cycles, we repeat it, because that is kind of at the lower threshold cycle, so we repeat it to confirm that it is positive,” Mancini said.

Me: Are there any positive samples that you’ve seen after 30 cycles?

Mancini: “We do occasionally get some between 30 and I’d say 33, but like I said they are repeated.”

“We go back to the original swab, pull off more of that liquid, and start the process completely over.”

“I can say that there’s a lot of conversation out in the world about threshold cycles. And as you get closer to 40, it’s a really low infection. But I have honestly never seen anything past 32, 33 Ct’s in our laboratory.”


Other non-PCR testing that UniPath Lab offers

Me: What other viral infections does your lab test for?

Mancini: “We do herpes infections, VZV infections, HPV infections,” he said.

Me: With those other tests that you do. Do they all test for live, viral infections, or do they differentiate between the presence of live or dead virus?

Mancini: “There’s no real way to differentiate them, period, because when you’re looking for the DNA RNA, all you can say is that the virus is present in the sample that you received. Whether it’s dead, whether it’s alive, I mean, the whole dead or alive for a virus is up for debate whether a virus is alive in the first place. A virus requires a host to replicate and all that. That’s a very loose definition of dead or alive.”

How long does viral RNA stay inside of a person? Depends on who you ask

Differing from the claim of UniPath’s Operations Director Jonathan Mancini that the virus may stay in the human body for a few days to a week is the claim from Michelle Roach, the Operations Director of Cedar Diagnostics.

“Once you test positive for PCR (methodology for testing for COVID-19). If you came in two weeks ago and tested positive for PCR, we really don’t recommend people coming back and testing again. Because people can shed for up to three months,” said Roach. “If they’ve gone through their 14-day quarantine then that person is considered through their active virus period. So it would be a waste of resources to have somebody come back in and test at two weeks and four weeks and six weeks or whatever to see if they’re still testing positive. We wouldn’t want to waste those tests.”

A follow-up phone call and voicemail to Roach requesting further information was not returned.

My written request for an interview with Sara Sawyer, Ph.D, a virologist working for the University of Colorado, was stonewalled.

Adam Howell is an unaffiliated voter and writer who believes in the constitution and accountability for all. He can be reached with feedback by clicking on this link to the contact page.

Addendum – Corman Drosten Review Report by ICSLS-11-01-2021
EUA-Thermo-TaqPath-ifu



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