Some follow-ups to this thread from yesterday about a Perspective article of mine, on early COVID cases in Wuhan, released by @ScienceMagazine :

First, I have learned that @franciscodeasis had earlier concluded that Mr. Chen, the so-called "Dec 8" patient, actually became ill on Dec 16:

And @Drinkwater5Reed and other DRASTIC members had advanced additional research along the same lines, including of the same news video I analyzed in my paper:

Kudos to all. I believe my additional insights into why the discrepancy may have arisen - surprisingly because Chen appears to have had a dental problem and fever Dec 8-9, are a useful new step.
And I'm happy to be bouncing additional ideas back and forth with @franciscodeasis and @Drinkwater5Reed currently.

On that note, here is a link to a translation of said video report, with Mr Chen's case starting at 12:30:

dropbox.com/s/3swu4gskv8rx…
From the timeline legend of my paper:

"A medical record from 9 December, shown in reference S4, states that the patient “has had a fever for one day [发热1天]” and prescribes two antibiotics, cefmetazole (头孢美唑), and piperacillin sodium (哌他). "
"The 9 December record is shown immediately to the right of a record from a doctor or dentist named Wei Tian (田巍)diagnosing “retained baby teeth [乳牙滞留]” and recommending “removal [of the baby teeth] under local anesthesia [局麻下51拔除]."
"Both records appear to be part of the same patient chart. This suggests that the fever started on 8 December, possibly due to a dental infection. This may have been the source of the confusion that led to the apparently erroneous 8 December onset date. "
"When talking about COVID-19, the patient makes clear in his own voice that his fever started on 16 December, at around 10 AM. This is a clear indication that his earlier symptoms, including his fever from 8-9 December, were not considered by him to be related to COVID-19:.."
"...if he believed his 8-9 December fever was the start of his COVID-19 symptoms, it is difficult to understand why he would state that his fever “began” on 16 December."
It has also just become clear to me that Ms Wei, the seafood vendor from Huanan who is now the earliest known case of SARS-CoV-2, had symptom onset Dec 10 at the latest. Someone reached out over email and provided this translation of this video:

thepaper.cn/newsDetail_for…
我是怎么染上的?我是这样的
How did I get covid? This is me
我是觉得自己有点累吧 往年也是这样的 今年要说还不累 还不是那么累
I felt a little bit tired. But I was like this last year too. This year's (business?) wasn't that exhausting, it wasn't too tiring
就是以前每年冬天总会有点流感什么的 我当时以为是流感 就是身体不舒服
every winter I will always get the flu or something. I first felt it was flu, I just wasn't feeling well.
头昏脑胀 感冒的感觉 蛮轻微
I head headaches and dizziness. Felt like a cold. Was mild.
没有什么蛮重要的表现 我一直从11号开始不舒服
It didn't really have any significance. I started to become (more?) uncomfortable starting on 11th
就去(小诊所)打针 打了两针之后就没有反应
I went to the local clinic to get shots.
This is now consistent with a report I cited from the @WSJ, which had her onset as Dec 10. Seems like that is likely correct.

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More from @MichaelWorobey

19 Nov
I feel I must reply to a comment from @DavidRelman in a recent @nytimes article on a piece of mine in @ScienceMagazine on why a careful analysis of the earliest known cases in Wuhan indicate that the pandemic started at the Huanan Market.
“It is based on fragmentary information and to a large degree, hearsay,” David A. Relman, a professor of microbiology at Stanford University, said... “In general, there is no way of verifying much of what he describes, and then concludes.”
Here is the article, for those who would like to test David's dismissals against what I actually present in the piece. I do hope you'll do so.

science.org/doi/10.1126/sc…
Read 14 tweets
18 Nov
I wrote a Perspective on the origin of COVID just released in @ScienceMagazine

science.org/doi/10.1126/sc…
I have spent the last few months trying to poke holes in the hypothesis of a natural origin of SARS-CoV-2 by asking:

Was the apparent preponderance of early cases linked to Huanan Market real or just a mirage because that is where people were looking for cases?
This is a key question, because if the pattern is real, it is *very* hard to explain why we would observe it if the outbreak had not started at the market, in particular the western section where illegal wildlife like raccoon dogs was sold. It's about the size of a Home Depot.
Read 17 tweets
5 Nov
1/11 It's a great day! Pfizer's new SARS-CoV-2 antiviral cuts deaths by about 90%

But it's also a good time for a thread about the evolution of antiviral drug resistance.

apnews.com/article/corona…
2/ In 1987, FDA approved the first HIV antiviral, AZT. Hope quickly turned to despair though, because in patient after patient the virus quickly evolved to become resistant to AZT.

It wasn't until 1996 that the key breakthrough emerged.
3/ At a conference in Vancouver BC, researchers revealed that if patients were given "triple therapy", cocktails of drugs that attacked HIV in different ways, resistance could be averted.
Read 11 tweets
1 Oct
1/ Medium thread on #SARSCoV2's furin cleavage site and a strikingly similar region in some of the new BANAL genomes from Lao, and in RmYN02 from China.

Seems worth trying to clear up the confusion of @ydeigin on this issue (even it means broadcasting my pic, below).
2/ The furin cleavage site of SC2 is the RRAR in the NSPRRAR stretch of amino acids in the alignment I'm holding up there. It is what makes the virus 'pop' in humans.

The BANAL viruses have NSPAAR. A couple other ones, including RmYN02, have NSPAAR or NSPVAR.
3/ So, having barely scratched the surface of the genetic diversity of these viruses in the wild, we've found several that are literally a *single* amino acid away from having a furin cleavage site.

For example: (NSP) ->inserted R<- AAR.
Read 11 tweets
15 Sep
1: A thread connecting the dots between:

(1) @PeterDaszak et al's fascinating recent preprint on the *many* SARS-related CoV infections in humans per year in Southeast Asia, and

(2) The furin cleavage site of SARS-CoV-2, and

(3) Why Wuhan?

medrxiv.org/content/10.110…
2: The study uses a clever combination of data streams to estimate that 400,000 people per year are being infected by SARS-related coronaviruses.
3: The authors note that not all of those infections are likely to be transmissible human to human

I strongly agree with this. We would see multiple new pandemic origins every year if even 0.1% of these were viable human to human pathogens.
Read 15 tweets
4 Sep
1: I want to follow up the thread below with some additional clarification of why we hypothesize that there may be no real #SARSCoV2 genomes transitional between lineages A and B.

2: @daoyu15 has written a thread asserting that we "toss any genomes that don't fit your conclusions away". I'm afraid this is incorrect on multiple counts.

3: What we show is that many of the putatively transitional genomes bear obvious evidence of being artefacts - probably due to bioinformatic pipelines, rather than sequencing errors per se. (Issues like calling a site with poor coverage to be the base of a reference genome.)
Read 13 tweets

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