Tag: medicine

COVID-19 Testing

Pooling is good:

If we look at this from the view of whole-population biosurveillance after the outbreak period is over and we have a 0.1% base infection rate, pools of 32 samples have an expected number of tests per person at 0.0628 or a 15.9x multiple on throughput/cost reduction.

Not even people dying left and right causes organizations to abandon the rules. Third world processes: Because of privacy concerns, the company’s call center does not leave voice messages. Its operators call back only 2x before moving to the next patient.
There’s also a lot of wishful thinking about serology tests:

There is no “serology test” – there are millions of possible serology tests, which need to be carefully compared and characterized to select ones that do more than just show you if some antibody against the virus is present. Reliable titres are going to be essential in the next phase of understanding this new viral infection – identifying who has protective immunity.

FDA delenda est

An innovative testing program in the Seattle area — promoted by the billionaire Bill Gates and local public health officials as a way of conducting wider surveillance on the invisible spread of the virus — has been ordered by the federal government to stop its work pending additional reviews.

Frequent, fast, and cheap is better than sensitive:

when you compare testing regimes it’s hard to come up with a scenario in which infrequent, slow, and expensive but very sensitive is better than frequent, fast, and cheap but less sensitive

Bill Gates is not impressed:

The majority of all US tests are completely garbage, wasted. If you don’t care how late the date is and you reimburse at the same level, of course they’re going to take every customer. Because they are making ridiculous money, and it’s mostly rich people that are getting access to that. You have to have the reimbursement system pay a little bit extra for 24 hours, pay the normal fee for 48 hours, and pay nothing And they will fix it overnight.

Titrating Quarantine

Last week I predicted that this might look like titrating quarantine levels – locking everything down, then trying to unlock it just enough to use available medical capacity, then locking things down more again if it looked like the number of cases was starting to get out of hand. This would eventually develop herd immunity without overwhelming the medical system. A paper argued for alternating periods of higher and lower quarantine levels based on how the medical system was doing:

A seesaw pattern of quarantine might work

Genomic epidemiology

We believe this may have occurred by the WA1 case having exposed someone else to the virus in the period between Jan 15 and Jan 19 before they were isolated. If this second case was mild or asymptomatic, contact tracing efforts by public health would have had difficulty detecting it. After this point, community spread occurred and was undetected due to the CDC narrow case definition that required direct travel to China or direct contact with a known case to even be considered for testing. This lack of testing was a critical error and allowed an outbreak in Snohomish County and surroundings to grow to a sizable problem before it was even detected.

this is a great summary of the state of the art on using mutations to reconstruct how a disease spreads.

COVID-19 Scenarios

One unlikely but possible scenario is that this “novel” virus is not really novel. Because its symptoms are generally mild and very similar to other symptoms from flu and other viruses, it may have been circulating around the globe for a while, without a name. It can be transmitted by people who have no symptoms at the time or even while they have the virus. If the majority of people infected don’t ever get sick, but easily pass it on, then it can spread widely unseen. But a few are susceptible to it and die. Because the symptoms are not unique to it, this illness is assumed to be flu or something else. Then something happened in China to produce notice — maybe someone created a test for it — and then as people died, the new test found many people positive.