The one thing that everyone agrees on, from doctors, to public health officials, to clueless newspaper op-ed writers, to clueless economic bloggers, is that mass testing for Covid-19 should be a national priority. The case is obvious: to control the spread of the virus, we need to know who has the virus and isolate them. And to return to work, you need to know your colleague is not going to infect you, so everyone at works needs to be tested. Everybody gets tested weekly, and voila, the country gets back on track.
Given its national importance, you would assume that somewhere in the bowels of the United States government there is a small group of smart, highly trained, and dedicated team of professionals working behind the scenes to make this happen. And you would be wrong.
Instead, the response is being lead by the group of criminals, incompetents, bootlickers, and general misanthropes who are intent on using the crisis for financial and political advantage. Their leader, the president, would condemn tens of thousands to die to save his ego, $50, or 150 votes . Again, no serious person can disagree with these obvious statements.
The most serious problem is that, incredibly, but not surprisingly, there is no overall plan to contain the virus. With no overall virus strategy, of course there no plan for the rollout of mass testing. We will have to rely largely upon the uncoordinated movements of hundreds of private companies, local and state governments, and the federal government. Somehow, grasping in the dark, with limited resources, they will have to make do.
And the results are, tragically, just what one would expect. The response of the CDC can only be described as a bureaucratic farce. The American health care system was designed suck the financial blood from the stones that are its patients, not to heal the sick. Our American Chernobyl lurches from one disaster to the next. In these trying times I truly feel for the cognitive dissonance Americans are facing who believe we have the greatest health care system in the world. They should be receiving hazard pay.
After the CDC failed to widely distribute a test kit, dozens of private companies have developed their own and are now ramping up production. Until the past few days we have only had the capacity to test individuals that are hospitalized and health care workers. We have now recovered somewhat, and we are now running about 65,000 tests per day, but the system is creaking. There are long backlogs in testing labs, and serious shortages of the basic materials that labs need to run the tests.
Will the system be able to ramp up to mass testing fast enough? That depends if the companies can increase production fast enough, and if the supply chain holds up. Public health officials have called for 150,000 tests a day, or 4,500,000 per month. For “mass testing”, the ability to test everyone in the United States over the course of a year, that would mean 27.25 million tests per month.
The supply situation
Testing capacity is currently limited by the number of tests kits and associated equipment available, as well as the lab technicians and machines needed to run the tests. Until recently the US only had capacity to test patients hospitalized for coronavirus and health care workers. Only in the past few days has testing been expanded.
The task of running a single test is not straightforward, and consists of a number of separate processes:
- Swab the nose of throats with test swabs
- Put the swabs in vials with growth media
- Vial transported to lab
- Technicians extract the virus’s RNA using test extraction kits
- Technicians use reagents to turn the RNA into DNA and to amplify the DNA
- A PCR test is run, which takes time and materials
Some of the steps can be automated. Expensive automated systems can run many tests at once, but their prohibitive cost means they must be kept in centralized locations that samples are sent to. Smaller testing systems are also available, which may be able to tested at the point of care.
Each of the components in the supply chain have their own complex manufacturing process and their own bottlenecks. Bottlenecks in several areas of the chain are currently preventing widespread testing. Even when samples are taken, there are backlogs in laboratories and it often takes 3 or 4 days to get a result.
The is currently a serious shortage of the test swabs that collect virus sample from patients.
The major manufacturer of test swabs is Copan, which has its headquarters and manufacturing facilities in Lombardy, Italy. US government has been airlifting about a million of the swabs per week.
The other manufacturer is Puritan, located in Guilford Maine. They produce a million per week. They are extending its five days a wekk schedule to six days, and running “at least” 20 hours a day. Biggest challenge for Puritan is a shortage of workers.
Swabs are transported to the lab in transport a transport medium, which is also experiencing shortages.
There is still a serious shortage of test kits.
Extraction kits are now made by a number of companies, including Roche, Quiagen, Thermo Fisher. The extraction kits use reagents with fairly complex chemicals.
Roche currently ships around 400,000 test kits a week to the United States, or 1.6 million per month. Roche is also ramping up its production. Roche’s kits only work with its proprietary machine. The fully automated test can deliver 384 results per eight-hour shift on its cobas 6800 system, and 960 on its larger cobas 8800.
Thermo Fisher’s TaqPath COVID-19 Combo Kit on its Applied Biosystems 7500 Fast Dx real-time PCR hardware in certain high-complexity laboratories nationwide. It can produce about 5 million per month. It plans to initially distribute the available tests to about 200 labs in the United States. Thermo Fisher is based in Waltham Massachusetts.
Qiagen currently produces about 1.5 million kits per month, hopes to produce 6.5 million per month by April, and 10 million per month by June. Qiagen is ramping up its production. These are global production numbers, however, and it is unclear can be used in the United States.
Hologic expects to produce nearly 600,000 of the tests every month by April. Massachusetts based Hologic manufactures the kit assays in San Diego, where it has 900 employees. Hospitals and labs can run the test on Hologic’s Panther Fusion platform, which in a 24-hour span can process up to 1,150 coronavirus tests.
Extraction requires extraction reagent, which are experiencing the most supply pressure. Companies are starting to ramp up their production of reagents. To get around this supply shortage, some hospitals have created their own extraction kits that use different reagents.
In order to test for the virus, need to convert the RNA into DNA, and then to amplify the DNA. Both need reagents. There are currently shortages of these reagents.
Transcriptase converts RNA to DNA. Primers — short stretches of DNA designed to match up with the viral genetic material — latch onto DNA.
Labs themselves need to source everything else to run the tests. This includes hardware: vortex mixers, microcentrifuges, specially-treated tubes, specially-designed racks, micropipettes to squirt tiny bits of liquid from place to place.