1/ this is the most detailed description of the lab-leak hypothesis I have seen (and I don't buy it)

It posits a "chopped-and-channeled version of RaTG13 or the miners’ virus that included elements that would make it thrive and even rampage in people?"
nymag.com/intelligencer/…
2/ to be clear, I've seen first-hand-in a 7 month-old baby-the scourge of a lab-produced bioweapon that was exfilitrated (anthrax 2001).

I agree w @mlipsitch position that the risks of creating Gain of Function pathogens w increased infectivity/deadliness outweigh the benefits ImageImage
3/ beyond artful prose and connect-the-dots suggestions, here's the idea:

That a bat virus sample (RaTG13) was manipulated in Wuhan lab to be more infectious through the lego-block addition of key genetic mediators of human infection

But that's not what the sequence looks like Image
4/ it's been a long time since I worked in a molecular biology lab or looked at GenBank sequences, but this isn't the pattern you would expect in the "chop shop" hypothesis

There aren't largely conserved areas with a few small regions inserted, this looks like evolutionary drift Image
5/ in my experience, lab scientists work with tools that are worn smooth by repeated use in their hands (it's hard to get things to work!)

In any accidental lab release you would see the signatures of the sequences most often used by that lab in their prior published research
6/ That's not what we see with COVID-19.

There are alternative lab explanations I'd believe

Is it possible that it was a new virus brought to the lab, whose sequences were not placed in public repositories, and which escaped into Wuhan?

Sure. (that's not bio-engineering)
7/ Is it possible that this was produced in a "dark lab" which did not publish their research or place sequences in public repositories?

Sure. But that's the whole reason why the US Government would fund these efforts worldwide, so we can have visibility into what's happening

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More from @Farzad_MD

1 Mar
1/ It took us over 6 months to have the epi studies that answered these questions.

That's one of the less recognized failures of an institution I revere, the CDC

They should have sharpened the questions, designed the studies and put dedicated epi resources behind them, quickly
2/ It took forever to do a proper serosurvey, to answer the IFR/CFR question

Understanding the primary role of asymptomatic spread was a game changer, took 6 months?

We are *still* debating kids as vectors.

Do we really know if vomiting indicates COVID?
3/ a few months later, we had other questions that needed answering-

Are we improving on timeliness of testing? 

Are we protecting the elderly? Where? (how?)

Is IFR declining within age groups?

Where were the focused surveillance activities to answer these key questions?
Read 5 tweets
22 Feb
1/ COVID has been a public health catastrophe

500,000 extra deaths, taking an average of 13 years each- 6.5 million years of life lost

That dropped US life expectancy by a full year

Did we erase a decade of progress? Will a child born today live a year less than last year?
2/ At first blush, it can seem confusing.

If life expectancy dropped by a year for 320 million Americans, shouldn't that translate to 320 million years of life lost, not 6.5 million?

OTOH, I trust the CDC. Here's the paper cdc.gov/nchs/data/vsrr…

seems legit. so what gives?
3/ Here's some more data- why did life expectancy plummet in 1917-1918 (by 10 years!) then rebound completely?

Life expectancy is the average number of years a group of infants would live if they were to experience prevailing age-specific death rates throughout their life
Read 8 tweets
29 Jan
1/ Please send all your #HealthIT eAsy fiXeS to @mickytripathi1

He'll love receiving & responding to them

The more the merrier! Make sure to include "just"

I'll start! ("likes" will demand a thorough response from @ONC_HealthIT)

>You should just get everyone on the same EHR<
2/

>You just need to create a universal patient identifier<
3/

>You just need to stop messing with the free market, industry will figure it out<

And introducing my guest speakers @DavidBlumenthal @HealthIT_Policy @HealthPrivacy @Fridsma @amalec @claudiawilliams
Read 5 tweets
23 Jan
1/ The Denmark variant story was pointed out by several people as being quite concerning- this line struck me - "Cases involving the variant are increasing 70 percent a week in Denmark, despite a strict lockdown"

But the actual data was hard to pin down- so I dug it up
2/ "The U.K. variant was 2 percent of sequenced coronavirus cases the last full week of 2020. By the second week of January, it had risen to 7 percent."

But in the context of declining cases what does that mean?

No link to data in article but it's here: covid19genomics.dk/statistics
3/ But those aren't actually the true cases, cause despite the headline "Denmark is sequencing all coronavirus samples..." while they are *trying* to sequence all, the number of cases with a genome of sufficient quality relative to the total number of cases ranges w-w from 10-36%
Read 7 tweets
11 Jan
1/ read this @adamcancryn @tylerpager piece, and let's discuss some of the points raised

‘There is a palpable concern’: Biden presses advisers over 100 million Covid shot goal politi.co/2XHhk1f
2/ first, I am so glad @JoeBiden *is* putting a hard to reach goal out there

When @matkendall and I set our first public targets
@ONC_HealthIT a longtime fed told us "never give them a date AND a number"

It's risky, it's gutsy, and it's the right thing to do for the country.
3/ It will be very hard to hit 100M in 100 days

But the very fact that this article was written EVEN BEFORE THEY START points to the intense focus it brings.

The new admin may miss their first big test, but vaccinate tens of millions more than if they shunned responsibility

🇺🇸
Read 12 tweets
30 Dec 20
1/ People are hardwired to get infuriated when they see injustice.

But I fear that applying this lens to covid vaccine distribution will lead to more deaths not fewer.

Stanford has screwed up, again. Some people who shouldn't have gotten it, did.
nbcbayarea.com/news/local/rac…
2/ What's the natural response then, from those all the way down the distribution chain, from state administrators to hospital execs worried about "wrong people" getting vaccinated first?

You spend more time collecting data, parsing into finer and finer gradations

You slow down
3/ Hospitals and nursing homes don't release more to staff until every i has been dotted.

States don't release more to hospitals and nursing homes until they've used up allotment

feds don't release more to states

Amidst a vaccine shortage, available supply sits in warehouses.
Read 8 tweets

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