Alina Chan Profile picture
17 Nov, 4 tweets, 2 min read
“if a similar phenomenon of host adaptation had occurred upon its jump into humans, those human-specific mutations would likely have reached fixation.. before the first SARS-CoV-2 genomes were generated.” 🙏🏻 ⁦@LucyvanDorp⁩ ⁦@BallouxFrancoisbiorxiv.org/content/10.110…
"The secondary host jump from humans into minks offers a glimpse into the window of early viral host adaptation of SARS-CoV-2 to a new host that has likely been missed at the start of the COVID-19 pandemic... and point to rapid adaptation of SARS-CoV-2 to a new host." 💯🔥
"pandemic is understood to have been caused by a unique host jump into humans from a single yet-undescribed zoonotic source in the latter half of 2019"

How does this fit with: "human-specific mutations would likely have reached fixation.. before the first SARS-CoV-2 genomes" 🤔
Is the hypothesis that a single natural spillover occurred, after which there was only 1 surviving lineage that led to COVID-19? All other adaptations to human died off or have not been detected? I guess China could've been that effective at wiping out all COVID in their country.

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More from @Ayjchan

18 Nov
On the covid data sharing debate, I believe that the context of a raging pandemic killing millions of people should be considered 1st. If a scientist finds that there is rapid virus adaptation in minks, must they seek permission or wait for the data providers to publish first?
I know that some scientists on both sides of this issue think that the same data sharing protocol applies to pandemic data as it does to non-pandemic data. But I don't think so.

Pandemic data should be shared in real time, analyzed in real time, publish/preprinted in real time.
In non-pandemic times, it makes sense to let the data provider take precedence; no urgency.

But in pandemic times, if you can do the analysis differently, faster, or better, shouldn't it be released ASAP? Especially if data is already shared only months after sample collection?
Read 5 tweets
17 Nov
Pandemic rages. Meanwhile scientists are fighting about what open data sharing means and whether you can publish analysis using someone's data if part of their dataset has not yet been published.
For a layperson, what is the issue here?

Scientists often keep data private so that they can publish in high impact journals and avoid others beating them in the publication race.

If you share data pre-publication, others are likely to swoop in and you lose your advantage.
In the pandemic, we've seen scientists really step up their data sharing generosity. It's the only way global databases @GISAID, public resources @nextstrain @CovidCg can provide big picture, powerful analyses of SARS2. So many analyses have been run on unpublished sequences.
Read 8 tweets
16 Nov
It looks like the universe will not let me have a day off.

@Nature just released an Addendum on the WIV's first paper about COVID, explaining what's up with RaTG13, the bat coronavirus most closely related to SARS-CoV-2. nature.com/articles/s4158…
tldr from the Mojiang mine, 293 CoVs found, 9 were SARS CoVs, 1 was RaTG13 first published in 2016 (not cited in their original 2020 @Nature paper). The other 8 SARS CoVs? We have no insight to their sequences!
Why are we hearing about this in mid-Nov 2020 when their paper was released in January, saying that they first found a match in the RdRp between RaTG13 and SARS-CoV-2 and then full genome sequenced RaTG13 to find a 96.2% genome identity match?
Read 20 tweets
14 Nov
@washingtonpost Opinion article by their editorial board.
"there are troubling questions in China that must be examined, including whether the coronavirus was inadvertently spread in an accident or spill from the Wuhan Institute of Virology" washingtonpost.com/opinions/globa…
@washingtonpost @PostOpinions I wanted to point out that the @TheLancet commission to identify COVID origins is chaired by the president of @EcoHealthNYC who has a massive conflict of interest wrt the WIV.
I have concerns regarding how rigorous and productive @TheLancet 's investigation of lab origins will be. Considering that Dr. Daszak did not even know until recently that the closest full virus to SARS-CoV-2 had been actively sequenced in the WIV between 2017-2018.
Read 8 tweets
14 Nov
Will do a thread today explaining the different types of covid tests, how they work, and what this means for false positives/negatives. fortune.com/2020/11/13/elo…
The first thing is to see what this virus is- at its core, it stores its genetic material, RNA (no DNA). This RNA is the blueprint for all of the proteins shown in this picture: N which wraps the RNA, the spike which sticks out from the virus and binds host cells, M, E etc.
Sorry, quick caffeine break. I overestimated my Saturday morning energy levels.
Read 38 tweets
12 Nov
Accelerated Evolution of SARS-CoV-2 in an Immunocompromised Host - reading for tomorrow nejm.org/doi/full/10.10…
Being a nerd, the first thing I did was to check if all of the spike mutations in the covid patient with "accelerated evolution" have been detected before in the 200K+ SARS-CoV-2 genomes on @GISAID using the @CovidCg browser covidcg.org
nejm.org/doi/full/10.10…
The answer is yes, all of the spike mutations shown in their figure except for N440D have been seen before, albeit there are other mutations at N440 (Y or K) that have been detected.

🤟@atchen_ for designing these SNVs to look like jellybeans @CovidCg covidcg.org Image
Read 6 tweets

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