Dolt 45

As I’m trying to dig out the problems with SARS-CoV-2 testing the United States, it’s become necessary for me to learn a bit about how the test works. I am not an expert in RNA analysis, but this is chemistry, which I do understand. I asked Stephen N. Floor, Assistant Professor in the Department of Cell and Tissue Biology at the University of California, San Francisco, some questions and to check my work. All errors and political content in this post are mine.

I am working from the CDC instructions for the kit and their information for laboratories using the kit.

From the point of view of the person being tested, samples are taken from their respiratory tract, which means having the interior of one’s mouth and nose swabbed and perhaps washed out. They might be asked to hack up some sputum.

The laboratory procedures are demanding, but standard for RNA and DNA work.

RNA is extracted from the patient’s samples. It appears to be the extractant for this step that is currently in short supply. The extractant may be TRIzol, a solution of phenol and guanidinium isothiocyanate, neither of which should be hard to supply.

A primer and standard are added to the prepared sample, which is then run through a PCR machine.

PCR stands for polymerase chain reaction, which is a method to make many copies of DNA. Because this virus is an RNA virus, its complementary DNA is produced, a dye is added that binds to the DNA, and the primer amplifies the SARS-CoV-2 selectively. Neither the virus RNA nor DNA is infectious, because they lack the rest of the virus.

The dye fluoresces, and the amount of fluorescence indicates how much DNA is produced. A control is added to give a known result, against which the SARS-CoV-2 result can be evaluated.

A test like this must be reliable – not too many false positive or negative results. False negatives are the more dangerous in this case, because they may result in an infected person moving about the community or a delay in treatment for a sick person. I haven’t been able to find statistics on false positive and negative rates for this test. The New York fact sheet has a short discussion of their effects.

If the sample from the patient is run through the procedure immediately, results can be available within several hours.

Despite administration promises, test kits continue to be in very limited supply, and the number of qualified laboratories and total tests small. (But numbers are all over the map, and the government doesn’t seem to be collecting them.) The reasons for this remain murky. It looks to me like a bad decision, possibly a number of bad decisions, were made early on, including not using the WHO kit and developing a kit to detect multiple coronaviruses rather than just SARS-CoV-2. This could be an organizational problem – I worked for an organization that felt it had to develop all its own computer codes, including payroll. That did not go well. Or it could be that Trump’s strong desire to deny the epidemic affected the judgement of people like Robert Redfield, CDC director.

People need to know if they’re infected so that they can observe quarantine or go about their business; doctors need to know so they can isolate patients and give them appropriate treatment; and we all need to know to understand the patterns of infection in society and take appropriate distancing measures. Right now, with so few tests, we have people self-quarantining, possibly without need, and people who don’t know they’re infected.

Also with PCR, the full genome of the virus can be sequenced, and that has been done in some cases. Trevor Bedford has an extremely informative Twitter account (@trvrb), where he explains what can be deduced about the spread of the virus from its genome.

Seven new #SARSCoV2 genomes from Washington State were shared today by @UWVirology. These group alongside existing genetic diversity so that all 23 community cases fall into the same transmission chain. 1/2https://t.co/1aeNEABy6q pic.twitter.com/Z245sIILBC

— Trevor Bedford (@trvrb) March 12, 2020

The media need to ask better questions on the lack of tests, particularly of Redfield and Mike Pence:

• Who made the decisions on which test to use? Why did they make those decisions?
• The question on the decisions is the central one, but you might be able to get there by asking about the alleged shortages of materials. Why? Who are the suppliers? Why are they not in short supply in the countries that are testing?

My suspicion is that the shortages are a cover for protecting Trump’s delicate ego. That priority has to be dumped in favor of the health of Americans.

Update: And it looks like my suspicion is right. From NPR Fresh Air interview of Dan Diamond, a reporter for Politico:

But at the same time, Secretary Azar has not always given the president the worst-case scenario of what could happen. My understanding is he did not push to do aggressive additional testing in recent weeks, and that’s partly because more testing might have led to more cases being discovered of coronavirus outbreak, and the president had made clear – the lower the numbers on coronavirus, the better for the president, the better for his potential reelection this fall.

Bolding mine. There’s more in the interview, but this is the most direct indictment of the president.

Cross-posted at Nuclear Diner

What Is The Test For SARS-CoV-2?Post + Comments (107)

Here are some early thoughts about what the Pence Task Force should do, coming out of my experience in project management.

Determine who is in charge. In Donald Trump’s typical desire to weaken subordinates and watch them fight, he has appointed three people as being in charge of the task force. No work will get done unless they agree who is to be the responsible decision-maker. Vice President Mike Pence, Secretary of Pharmaceutical Profit Alex Azar, or Ambassador Deborah Birx, MD. Once a leader is determined, all members of the task force must turn back Trump’s meddling on this issue.

As a part of setting up a responsibility structure, leaders must be chosen for subgroups as noted in the following topics.

Communications. Shut Trump down unless he learns something and can control his fear and inclination to improvise. Even then, his best play would be to act as a listener in his roundtable discussions and allow the experts to speak. Get a name for the task force: “Coronavirus Task Force” would do. Refer to it that way. Expert briefings every day, with no restrictions on video and recording. The topic of the briefing should vary from day to day, emphasizing recent developments. Lists of actions individuals can take should be posted on the internet and made available to local newspapers and governments. Hotlines should be set up. Communications should be accurate and should tell people what to expect.

Detection, treatment, and vaccine. Set up a National Academy of Sciences panel to investigate what went wrong with CDC’s development and distribution of detection kits. More urgently, decide on one kit and a recommended protocol for deciding who is to be tested. (This may have been done already, but they claimed it was done almost a week ago, and now it is being claimed again.) Make testing free to those being tested. Get the lab work on treatment and a vaccine out of the public eye. Report no claims until they are verified. Form a panel of experts to evaluate claims and recommend ways forward.

Community planning. State and local resources must be included in planning. The Public Health Service has a large role to play, although its funding has been greatly reduced under the Trump administration. Funding should be restored. Recommended standards must be developed for closing down events that involve large numbers of people or schools and for limiting movement of people within states or localities.

Maintaining essential services. Develop plans for maintaining garbage collection and availability of water and sewage services if large numbers of employees are absent because of illness. Hospitals need similar plans. Payment for medical services may need to be changed from emphasis on individuals. Grocery stores must continue to provide fresh food; plans must be made for people to access them.

Supply chains. There are three scales on which supply chains must be considered: international, within countries, and locally. Internationally, China supplies many pharmaceuticals and much medical equipment. Their shutdowns are affecting availability. International shipping is a vulnerable point, as airlines shut down flights. Essential chains (food, drugs, supplies to keep water, natural gas, sewage processing running) within the US must be identified and reinforced. Within communities, it may be necessary to set up food deliveries and monitoring of the most vulnerable in their homes.

Congress must be involved as well. Each subgroup must have a legislative liaison to the appropriate Congressional committees.

That’s a start. People who know more than I do about the specifics can fill in what I haven’t included. Would be good to hear from Pence and the task force that they are addressing these issues.

The White House Coronavirus Task ForcePost + Comments (213)