What is a public health test? A thread on population-level vs. individual-level optimal criteria (this is for a thread to be linked elsewhere so is probably quite incoherent)
From a clinical perspective we want a test that is optimal for helping the individual being treated. So we want to be as sure as possible that the result leads us to the right diagnosis and treatment
To achieve this, we might favour sensitivity and specificity above all else – those are the important metrics for treating our patient. We are probably happy to use a battery of expensive and time-consuming tests because we want to do the right thing for the person in front of us
But for a population, the optimal criteria may be quite different, because we are considering the outcome summed across many patients, not just one. Maybe we don’t have the resources to use the whole battery of tests on everyone...
... either we can use 3 tests on 10 people or 1 test on 30 people. Which is better from the perspective of the patient and which is better from the perspective of the population?
A toy example: say we are rolling many dice of different shapes. We have two strategies: either rolling 60x6-sided dice, or a 600x20-sided dice. Each person is a die, and the number of trials is our tested population. We get a “win” when we roll the highest number – a 6 or a 20.
If we take the perspective of an individual die (the individual-level metric), then we are better off being a 6-sided die. *I* only get 1 roll and *I* want it to be 6. *I* have a 1/6 chance of getting the max score vs. 1/20. That is the “individual-level optimal test”.
But across all dice, rolling a 6-sided dice 60 times *we* expect to get only 10 "wins". If instead *we* want to maximize the number of "wins" overall (either 6s or 20s), then rolling a 20-sided dice 600 times is a better choice, because we expect 30 “wins”.
A key additional factor for a communicable disease is that averting/treating infections is not only beneficial to the individual, but there is the knock-on effect benefiting everyone who is not yet, but COULD be infected. So we must factor that into our calculation.
To use the dice example, maybe we are allowed to roll an extra dice for each “win” we get. The 600x20 strategy becomes even better to maximize the number of wins overall – that is the “public health test”.
So the individual-level optimal approach is to use a 6-sided die. But the population-level optimal approach is to use many 20-sided dice.
I agree that the term "Public Health Test" is new without a rigorous textbook definition yet (AFAIK). But I think it's a useful framework, particularly in the context of an epidemic or pandemic. The term "Public Health Test" has a clear use and is distinct from a "Clinical Test".
Actually with these numbers the 6-sided strategy gives us slightly more "indirect wins", but you get the idea.

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More from @jameshay218

13 Feb
Ct values can be used to estimate epidemic dynamics UPDATE! Ct values are expected to change depending on whether the epidemic is growing or declining, and we harness this to estimate the epidemic trajectory. Lots of cool new analyses and methods! 1/12

medrxiv.org/content/10.110…
Highlights:
- Cts from symptom-based surveillance change over time, but the effect is weaker
- Methods to infer incidence using single cross-sections of Cts
- Unbiased by changing testing coverage
- Gaussian process (wiggly line) model for incidence tracking using Ct values
2/12
This work is *JOINTLY led* with @LeekShaffer and PI’d by @michaelmina_lab. Thank you also to the ever insightful @mlipsitch and to coauthors @SanjatKanjilal @gabriel_stacey and @nialljlennon. 3/12
Read 14 tweets
14 Oct 20
Ct values can be used to estimate epidemic dynamics! We show that the distribution of viral loads changes during an epidemic and develop a new method to infer growth rates from cross-sectional virological surveys without using reported case counts.

1/25

medrxiv.org/content/10.110…
Highlights:
- The distribution of observed viral loads is determined by recent incidence trends
- The median and skew of detectable Cts in Massachusetts were correlated with R(t), as predicted
- A novel statistical method to infer the epidemic growth rates using Ct values

2/25
Cts are inversely proportional to log viral loads. The relationship depends on the instrument and sampling variation, but low Cts generally indicate high viral loads. Think about expectations & distributions rather than individual measurements

academic.oup.com/cid/advance-ar…

3/25
Read 25 tweets
7 Oct 20
Very excited to share our updated preprint on pooled testing for SARS-CoV-2 surveillance. This has been a fantastic modeling and lab collaboration with @BrianCleary, @michaelmina_lab and Aviv Regev, and it’s all about our favorite topic: viral loads. 1/16

medrxiv.org/content/10.110…
Highlights:
-PCR sensitivity and efficiency are linked to epidemic dynamics and viral kinetics
-Prevalence estimation without testing individual samples using a few dozen tests
-Simple (by hand) strategies optimized for resource-constrained settings

Full story below. 2/16
We (the world) still need more testing. The number of test kits is still limited in a lot of places, meaning that we are missing a lot of infections, not testing regularly, and are flying blind wrt population prevalence. Pooling has been discussed as part of the solution. 3/16
Read 18 tweets
27 Mar 20
The lack of clinical COVID19 cases in children is odd. Understanding why will be essential in deciding which social interventions are most useful. We discussed this alongside a modeling analysis here: dash.harvard.edu/handle/1/42639…
@DrDJHaw @BillHanage @CJEMetcalf @michaelmina_lab
We propose 4 possible explanations for the lack of cases in children:

1) Kids haven’t been making as many contacts as normal. This may contribute, but probably isn’t the only factor: medrxiv.org/content/10.110…
2) Children are less susceptible to *infection* or adults are more susceptible. Seems unlikely now, given secondary attack rates from contact tracing, though conflicting findings: medrxiv.org/content/10.110… + previous
Read 10 tweets
25 Mar 20
A recent analysis from Oxford presented a range of model scenarios consistent with observed COVID death counts. I’m going to reproduce their analysis here and then present some slight modifications to provide a conservative (if technical) perspective. (gonna be 15ish tweets)
They showed you can estimate the same number of deaths with either a high % of the population at risk of severe disease and a recent epidemic start, or a low % and an earlier start. Some media outlets have reported this as suggesting “majority of the UK has already been infected”
But that’s *not* what the authors were trying to say. The aim was: given what we do know about the virus, let’s test different assumptions for the stuff we don’t know and see which tests are consistent with observed death counts.
Read 20 tweets
7 Mar 20
Total isolation isn’t the only way to reduce #coronavirus spread. Reducing unnecessary contacts (only invite the best people to your birthday party) helps. Based on school maths: if you roll a die 10 times, the probability of 1 or more 6s is 84%. If you roll it twice, it’s 31%.
This also applies if you reduce the nature of your contacts. For example, if you stop licking your friend’s face, maybe you go from a 6-sided die to a 20-sided die. Then the probability of at least 1 20 at your 2-mate birthday party goes down to 10%.
Even partial reduction goes a long way to reducing transmission below a critical threshold. R0 = prob of transmission on contact * infectious duration * contact rate. If we have R0 = 2 = 0.04*5*10, then halving the contact rate gets us to 0.04*5*5 = 1.
Read 4 tweets

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