The more I look into this, the more cases I see where the short-run scarcities and bottlenecks are the result of an FDA approval process for tests that is very specific about inputs — use these specific RNA extraction kits sold by these firms; these specific swabs…
As we scale up and hit a capacity constraint, the academic researchers seem to quickly identify workarounds, but it seems to take a long time for these to get throug the approval process - even for an Emergency Use Authorization.
So I keep having conversations where people close the existing testing system tell me that e.g. “swabs are a huge bottleneck” and then conversations with the researchers where they say, “you don’t need swabs, saliva works just fine.”
So we should distinguish two questions about scaling:
a) How hard to scale the FDA approved test, with an EUA amendment for each change?
b) How fast could the veterans from human genome project go if all they had to do was run a lot of tests that work?
The twitter thread version of my plan:
- Stop testing people with symptoms. Presume positive and isolate.
- Offer all frontline health care workers a quick turnaround molecular test for presence of the virus (RT-PCR or LAMP test). Isolate if positive.
- Offer the same type of test, which can identify asymptomatic spreaders, to every patrol officer who rides with a colleague. Offer the entire department the option of testing at the start of each shift.
- Extend to pharmacists. (EMTs should be included among front line health care professionals.)
- Extend to other essential workers such as transit workers. (FYI, > 40 employees of the MTA in NY have died of covid-19.)
- Do the math. Discover that you need millions of tests per day.
- When someone tells you that “we could never test that many people,” ask “ok, so your plan is to stand by and do nothing as asymptomatic spreaders kill their colleagues?”
- Note that people at Broad Institute say “Given the low cost and scalability of next-generation sequencing, we believe that this method can be affordably scaled to analyze millions of samples per day using existing sequencing infrastructure.”
- When people say, “SWABS!” tell them to talk to the people at Rutgers who are applying for permission to test saliva samples.
- When “REAGENTS FOR RNA EXTRACTION!” say that we can test for the virus without using the RNA extraction kits that were mandated as part of the original FDA approval of RT-PCR tests.
See papers in the last few days on bioRxiv describng work arounds to reagent shortage.
When you say “REAGENTS!” you have to make this face: https://t.co/MLwzj8R2uP
- When people say that we have to have an elaborate system for tracing contacts before we can move forward, point out that the CDC is saying we do not have to bother testing essential workers who are known contacts so shortage of contacts is not the problem we face.
- When you strip away all the noise and nonsense, note that once we cover essential workers, its easy test everyone in the US once every two weeks. Just do it. Isloate anyone who tests positlve.
- Check your math.
Surprise, R0 < 1.
Pandemic is on glide path to 0.
No new outbreaks.
No need for any more shutdowns.
Let everyone go back to normal.
- Check in on the folks who will still be arguing about how to implement some kinda sorta obligatory tracking system.
Ask them how they are doing with getting the members of QAnon comfortable with their scheme.
Lots of people who know nothing about molecular genomics make all kinds of confident preditions that it will be impossible to scale up molecular testing for SARS-COV2.
Just for the heck of it, see what a team that knows something has to say.
“Given the low cost and scalability of next-generation sequencing, we believe that this method can be affordably scaled to analyze millions of samples per day using existing sequencing infrastructure.”