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Michael Mina Profile picture
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14 Oct, 7 tweets, 5 min read
New research! Starring... Ct values!

We endeavored to ask:

Can we create a brand new metric to know if #COVID19 is increasing/decreasing without staring at case counts & fractions positive - both greatly obscured by test practices.

Yes! w/ Ct values!

medrxiv.org/content/10.110…
In this incredible Tweet thread 👆 @jameshay218 describes the new work - we hope will lay new groundwork for public health authorities to track this/future viruses & if control strategies are working

Work also w co 1st author Lee Kennedy-Shaffer, @mlipsitch & @SanjatKanjilal
One piece that is so cool about this method is we do NOT need a time series of case data to create a trajectory (those little bars on @nytimes website or google that we’ve all stared at for the past 9 months to see trend up vs down in cases). We can do it from a single day!

3/
As @jameshay218 explains in the thread (and we detail in the paper linked above) this is because of a neat property of exponential growth/decay where, on way up, +ve ppl are on avg infected more recently than on way down. And this is born out in the Ct values (viral loads)

4/
And this simple property is sufficient to determine the epidemic trajectory and growth rate.

IMPORTANTLY, this reinforces just how powerful the Ct value data can be (they are currently almost always thrown away!!). They are NOT just noise. We should record and use them.
.@apoorva_nyc @sciencecohen @RobertFService @robsteinnews @KatherineJWu

Thought you might be interested in this. Still in preprint stage👆
Mistakenly did not add Lee’s twitter handle. @LeeKShaffer co-first authored this piece (which remains a work in progress) with @jameshay218

The two of them have done a tremendous job. Can’t wait for the rest of the analyses (the really cool stuff) to be added to the preprint

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More from @michaelmina_lab

Michael Mina Profile picture
13 Oct
Important

This virus is not happening in a vacuum where no information existed previously

On Immunity, On testing, On serology, On transmission, On masks, On treatments...

We must stop this narrative that we know nothing of this virus until we learn it anew - again.

1/
The constant drum beat of “we do not know that yet” is tiring.

We KNOW SO MUCH! about SARS-CoV-2 and COVID-19. We knew it before this virus was ever discovered!

We’ve watched since January with study after study reaffirming out expectations of this virus in SO MANY WAYS.

2/
In many we ways we got lucky on this front.

Take HIV for ex. HIV was a new virus for which we generally did have to rewrite the text book

But this virus is different from HIV in that it is behaving in almost all ways per the “textbook”.

3/
Read 19 tweets
Michael Mina Profile picture
13 Oct
So important in this pandemic to NOT let RARE events make the headlines & grab our attention

@NPR - this should NOT be a headline unless you’re going to have daily headlines that say “Millions NOT reinfected today with COVID19”

People are scare enough

npr.org/sections/coron…
Re-exposures are essential to build our immune system. This is not in question. They are like training.

But like anything, when enough people get a re-exposure, there are going to be rare cases here and there that go awry and someone gets more sick the second time.

2/
But this is rare and should NOT be interpreted as people will not build protective immunity and that vaccines will not work.

The take away from this piece should be “In a rare event, a person in the US gets a severe second infection with SARS-CoV-2”

One other point

3/
Read 7 tweets
Michael Mina Profile picture
12 Oct
Trump tested negative on @AbbottNews BinaxNOW test. His MDs are using for evidence of no longer contagious

I don’t disagree - but like use of tests to stop transmission - this is just one piece. Frankly, in this context, it’s being used out of context...

1/
The most important point of deployable rapid tests are that they can be used by many people, frequently!

But should not be used as confirmatory testing of -ve PCRs. This doesn’t make sense and WH use for this confuses how these tests are most appropriately used.

2/
These tests should be to screen ppl (frequently) for +ve results to identify people likely needing to be isolated

In this case @POTUS has had numerous PCR tests and is the president! He can get a viral culture test if he wants to go out w confidence he is not contagious

3/
Read 5 tweets
Michael Mina Profile picture
10 Oct
IDNOW by @AbbottNews rapid test is what @POTUS uses

It's said to be poor w very low sensitivity - the news, @US_FDA and many others say so

But this is a mistake. It's a very good rapid test

I explain here at ~3:30
(Just found link from an old talk)

The short story is the main study from NYU that led to the low sensitivity claims used an extremely skewed sample set

If you remove from the paper just the +ve samples with a Ct value >40 (incredibly miniscule RNA loads), the sensitivity of the test jumps from 60% --> 90%!
If you take only samples with Ct values <38 (still on par w almost any other PCR test), then sensitivity jumps from 60% --> 95%!!

So the problem wasn't the test, it was the samples evaluated. 30% of them were at the very limit of detection of a SLIGHTLY better test
Read 6 tweets
Michael Mina Profile picture
8 Oct
Urgent @US_FDA @CDCgov #AndWhoeverWillListen

Rapid paper strip tests can be extremely powerful public health tools

But they cannot just be introduced without major information campaign AND clear algorithm for use - like the CDC HIV algorithm.

1/x
nytimes.com/live/2020/10/0…
Despite high sensitivity when someone is likely contagious, and high specificity relatively speaking - 98%,

When deployed widely, a 2% false positive rate (1 per 50) is too high.

2/x
If deployed alone, a pop screening tests with a 1 in 50 false positive rate will immediately create a lack in confidence of the assay. This is already happening!

I’ve said it before - directly to FDA/CDC and here - we MUST have a clear goal and plan for these tests.

3/x
Read 7 tweets
Michael Mina Profile picture
7 Oct
Winter is coming!

If we do not get this virus under control now, we are in for a perfect and terrible storm

We are not taking the expected seasonality of this SEASONAL virus seriously!

Instead, we've assumed our efforts are responsible for decreased cases this summer...

1/x Image
I worry very much that people are confusing the fact that this virus has transmitted in the summer for it not being very seasonal.

This is a grave mistake and misinterpretation...

2/x
The 'force of infection' of this virus is massive! Think of it like the momentum that the virus has to transmit

The huge number of susceptible people is what is allowing the virus to maintain transmission through the summer months - when other coronaviruses go to near zero.

3/x
Read 11 tweets

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