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What Happened at the CDC? Why are they conflating the antibody test to SARS-CoV-2 and the antigen test? Why did they produce their own COVID test and not just accept the WHO antigen test?

2020-05-21

CDC Headquarters in Atlanta by Ribastank courtesy of pixabay.com

What happened to the CDC (Centers for Disease Control and Prevention)?  It appears that political loyalty to the person of the Commander in Chief has elbowed aside scientific expertise and is causing terminal dysfunction in an organization that should be at the spear-tip of the global response to the SARS-CoV-2 pandemic.  American cooperation with the WHO (World Health Organization) is in jeopardy due to a political calculation by a chief executive with his eyes on re-election in November instead of on a robust response to a global pandemic that has already killed nearly 100,000 Americans and is sure to exceed that total by the first of June.

First, just so you know: scientists at Harvard Medical School in Boston (with nine monkeys) replicated a Chinese study published in March (with four monkeys) that shows rhesus macaque monkeys definitely develop complete immunity to re-infection with SARS-CoV-2.  The scattered reports of “re-occurrence” of infection appear to be in error.

I apologize in advance for the length of this post.  Please be seated and have a stimulating beverage on your table.

It is not widely known among Americans, but the US-CDC has been a model for government agencies in countries around the world.  The US government agency was so widely revered that its organization has been copied everywhere.  The agency proudly states that they support other countries in their efforts against many serious diseases, particularly Ebola, HIV, tuberculosis, and malaria (the latter two are the diseases that kill the most people around the world every year, just not in the US).

According to the Wall Street Journal (WSJ) in 2018, “The CDC currently works in 49 countries as part of an initiative called the global health security agenda, to prevent, detect and respond to dangerous infectious disease threats. … The package included $582 million in funds to work with countries around the world after the Ebola crisis in 2014 and 2015.”  Obviously that changed with the current administration and its emphasis on “America First”.  That leads directly to the answer to our question, “What happened at the CDC?”

The obvious problems in this pandemic started with the CDC’s decision not to use the SARS-CoV-2 antigen test that had been developed by the World Health Organization (WHO) and is being used in virtually every other country in the world.  Instead, they decided to develop their own test.  The test was first announced on February 3, and received Food and Drug Agency (FDA) Emergency Use Authorization (EUA) on February 4.  The EUA followed the announcement of a public health emergency on January 31.

At first, they did everything right: they created a real-time reverse transcriptase polymerase chain reaction (RT-PCR) test that had three components: one to identify the virus’ nucleocapsid gene one, one for nucleocapsid gene two, and one to identify human RNA-ase gene P.  Problems arose with the third component, which was contaminated when the test was scaled up for production by a separate lab.

The problems with contamination in the mass-produced kit made by International Reagent Resource (IRR) made the test unusable.  Apparently, appropriate procedures were not followed in production and the same isolation hood was used for two separate processes, contaminating a reagent with human DNA.  These problems were not corrected for weeks.  Since this test was the only one authorized by the FDA, no other clinical lab (even the ones that created their own tests) could legally test for COVID-19 during this period– most of the month of February, a critical blind spot, as it turned out.

The absence of a test made it appear as if there were no cases of COVID-19 in the US– despite the fact that labs knew full well that there were many patients who had the infection, due to their use of unapproved tests (but could not legally say so).  Research labs that did testing on non-clinical specimens, that is, tests that didn’t identify the patients that the samples came from, knew that there were cases.  At this time, there was plenty of influenza-like illness (ILI or just “flu”) to be had at clinics and emergency rooms, so early cases were dismissed as “flu”.

Only when the patient tested negative for actual influenza and other respiratory viruses did doctors have any notion that they were dealing with a new entity (although they suspected exactly that).  If you’ve gone to the doctor for the flu, you know that ordinarily little or no testing is done.  If you’re lucky, you’ll get a rapid test for strep throat (which you should because ten percent of sore throats are strep).  You won’t get a test for influenza, although they are available.  Nor will you get a test for the common coronaviruses that cause “colds” even thought these are also available.  You most certainly won’t get an acute serum blood test drawn to be saved for comparison to a test two weeks from now when you recover– how is the doctor going to justify that to the insurance company??  (I used to do that when I worked at a government clinic for Native Americans– but I was the only one.)

Now we have information that makes this month of February appear appear truly critical.  The first known case of COVID-19 in the US was in a patient who self-identified as being a novel coronavirus case (he read about the WHO alert in the paper) and came directly from Wuhan (the source of the outbreak)– he was hospitalized on January 21 and his case appeared in the New England Journal of Medicine (NEJM) on January 31.  The first known death from the new virus in the USA occurred in Santa Clara County, California on February 6 and was retrospectively identified by autopsy (which also showed the terminal event to be a massive myocardial infarction, a heart attack) — but this wasn’t announced until April 22.

Thousands of travellers to and from Wuhan, China entered and left the US between December and the end of January (when flights from China were stopped by presidential order, except for US citizens and their dependents).  We now suspect that many of these travellers were carriers of the new virus.  Travellers from the epicenter also went to Europe and seeded the infection there; the outbreak in New York actually began with a European variant of the virus rather than directly from China.

In the meantime, the CDC was asleep at the switch.  I suspect that the agency had been neutered by political appointees from the present administration, who sabotaged its functioning.  I have no evidence for this suspicion, just a feeling.  Of course, I trust my own feelings so much more than I trust the feelings of our current Commander in Chief.  This is because my feelings are informed by scientific information instead of real-estate information (whatever real-estate information is, or whatever Fred transmitted to his son and heir).

I could be wrong.  Judge for yourself.

The CDC created a “guide to re-opening” which wasn’t acceptable to the Commander because it was “overly prescriptive”.  It wasn’t released.  Instead, a pared-down, dumbed-down version consisting mostly of pictures and simple diagrams was given out, missing a critical component: advice to houses of worship.  Even this watered-down guide is being misapplied and isn’t being followed.  Apparently the Commander’s real objection to the CDC’s guide was that it told churches what to do– a no-no to his evangelical base, who only take orders from G_d.

Worst of all: I learned today, in a highly critical article from the Atlantic (titled “How could the CDC make that mistake?”) that the CDC has been conflating (mixing together) two different types of tests for the new virus: the antigen test, described above, and the newer antibody test.  The two tests give completely different information and have different levels of sensitivity and specificity.  The antigen test identifies acutely infected people starting a couple of days before symptoms begin (if symptoms occur at all): when contagiousness starts.  The antigen test continues to show positive for variable periods, generally about two weeks after infection has begun.  The antibody test, on the other hand, only becomes positive roughly two weeks after infection and stays positive for months, probably a year or more.

The antigen test is extremely specific, in part due to its careful makeup: it tests for two different parts of the new virus’ genome and controls for the presence of human genes.  It should be extremely sensitive, due to its inherent nature: a polymerase chain reaction is able to magnify and identify incredibly tiny quantities of genetic material.  Reports available early in the pandemic revealed that, in actual use, the test only identified 72% of actually infected patients when compared to tests using fluid obtained directly from the bronchi and lungs.  This fact has been glossed over, but has re-surfaced in criticism of the new rapid test used in the White House.  Claims appeared after two aides tested positive that the rapid test missed as much as half of the actually infected patients.  Those claims may be exaggerated, but it has not been widely understood that the antigen test is not as sensitive as we would wish it to be.

The antibody test is not as specific as the antigen test: there are circumstances, particularly when the infection is rare, in which the antibody test will be false-positive.  The antibody test also may not be as sensitive as we would want: some patients who have recovered may never show antibodies.  The antibody test is probably more sensitive than the antigen test.  We are also not sure that the presence of antibodies (or recovery from the infection) confers immunity to a repeat infection, although studies in rhesus macaque monkeys both in China and here in Boston do show immunity.

The problem with conflating these two tests in announcements is that they measure two different things.  They should be announced separately so we can have a clear idea that “this is the number of acute cases we have identified” and “this is the number of resolved cases we have identified”.  The problem with the CDC appears to be that some naive individuals involved in compiling test results for announcement don’t understand the difference and want to inflate the number of tests performed at the same time as they reduce the percentage of positive tests– for the publicity.  The same is true of several states that are doing the same thing (although some states corrected this when it was pointed out to them) — see the Atlantic article for details.

A separate problem, in Georgia, appears highly motivated: on a day they announced “re-opening”, Georgian officials displayed a graph that showed the dates all mixed up– with the result that the positive test results appeared to be going down daily when in fact they were fluctuating randomly.

This problem, the presence of naive individuals who clearly don’t know what they are doing, is typical of the current administration.  People are being selected for jobs based on their particular political loyalties rather than their expertise.  There is a shortage of people with actual expertise who have the desired loyalties.  The result is that people who have no experience in the needed areas are doing jobs for which they are not qualified and they are, to put it bluntly, screwing up.

I apologize again for the length of this post, but I have tried to put the point in the first paragraph: the CDC is being sidelined in a crisis when the expertise of their nonpolitical employees is really needed.  People who know what they are doing are being fired or transferred, almost literally, to the Aleutians (America’s Siberia, if you will).  Richard Bright, who has filed a “whistleblower complaint”, is only one example.

Need I go on?  I believe I have made my point.

 

 

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