Alina Chan Profile picture
Sep 25, 2020 17 tweets 9 min read Read on X
There's some confusion about how new the D614G mutation is. I'm going to use data on @GISAID visualized by @CovidCg to answer this question. The first time it appeared in China was Jan 23, 2020. So this mutation occurred pretty early on in the outbreak before travel restrictions.
When+where did D614G first get detected in Europe? It's not possible to tell using GISAID alone because many countries did not sequence virus isolates and deposit data till later in the pandemic. However, you can see that there are EU countries with D614G even in Jan.
It was only after January that travel restrictions started being sporadically imposed on China by other countries but it was too late because SARS2 (including D614G variants), as we now know, was already widespread. thinkglobalhealth.org/article/travel…
Had to remove the UK from the "Compare Locations" analysis in Europe because of how many sequences they've uploaded - just a tsunami that washes out the sequences from other countries. The G614 variants, in blue, are among the earliest sequences found in the UK, including in Jan.
Other European countries saw similar trends as well - D614G was among their earliest sequenced virus isolates and quickly became the more prevalent mutation at that point in the Spike. E.g., Germany shown here, G614 in blue, D614 in grey
Netherlands, G614 variants shown in blue, D614 in grey. Both present in the country since the beginning of the detected outbreak there.
What about countries that were able to curb the spread of COVID? Was it that they were dealt an easier hand of less transmissible SARS2? This is Singapore, D614G mutation was also detected in February, similar time as several European countries. Strangely, D614G did not dominate.
Visit covidcg.org to play around with the data yourself :) This is Taiwan, another country with exceedingly few COVID cases. They detected D614G as early as March but half a year later their country still hasn't exploded with COVID.
South Korea also saw the D614G mutation in March. In both the "Compare SNVs" (left) and "Compare Lineages" (right) mode, you can see how there were distinct waves of the virus in their country.
Japan also saw D614G early - at the end of January. It's by no means a new mutant of SARS2 for many countries. covidcg.org
Even across Africa, D614G has been around since the beginning. Worth pointing out again that it is not just 1 variant or strain of SARS2 that carries D614G. Many distinct SARS2 variants carry the same G614 mutation on top of several other mutations.
One particularly interesting country is Australia. At first glance it looks like D614G (blue) is dominating again. But turns out the new wave is marked more specifically by an S477N (pink) spike mutation. D614G+S477N were detected in Australia in late Jan. covidcg.org
New Zealand, another country that's done a phenomenal job limiting the spread of COVID. D614G has also been there since the beginning. The country was able to bring the new daily cases of COVID down to mostly single digits by late April.
How about states in the US? State name at top left corner of each picture. G614 in blue; D614 in grey.
US states started seeing D614G by early March. This was after China travel restrictions had been implemented early Feb, but EU travel (conferences!) was still ongoing. The Mar announcement of restrictions caused Americans to stampede back from EU (where D614G was rampant) to US.
“We closed the front door with the China travel ban,” New York Gov. Andrew M. Cuomo (D) said last month as officials began to grasp the magnitude of the failure. In waiting to cut off travel from Europe, he said, “we left the back door wide open.” washingtonpost.com/world/national…
For more ways to use our free and awesome resource @covidcg covidcg.org please check out our new preprint: biorxiv.org/content/10.110… enabled by @gisaid data contributed by hundreds of different labs around the world.

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More from @Ayjchan

Feb 5
There is speculation that US funded collaborations with the Wuhan Institute of Virology to keep an eye on virus research there.

The problem is that, when a pandemic happened, the middleman did not produce intelligence but also actively suppressed the lab leak theory.
When the SARS-CoV-2 sequence was released in Jan 2020, EcoHealth could've said
1⃣They planned to put furin cleavage sites in SARS-like viruses
2⃣In 2013, the Wuhan lab discovered a new lineage of SARS-like viruses that the covid virus belongs to
3⃣Work was done at low biosafety
Instead we had to go through 5 years of the lab leak hypothesis being painted as a racist, anti-science conspiracy theory and a ton of misinformation from EcoHealth about the work being done in Wuhan.
Read 7 tweets
Jan 9
No punches pulled piece on #OriginOfCovid by @ianbirrell

"The pandemic revealed the arrogant and contemptuous behaviour of leading scientific figures, aided by prominent academic journals, patsy journalists and weak politicians."
unherd.com/2025/01/chinas…
@ianbirrell I suggest one correction @ianbirrell please replace 'despite' with 'because of':

WHO "hired Sir Jeremy Farrar, despite the former Wellcome Trust boss’s exposure as a central player in... branding any suggestions Covid could have come from a laboratory as conspiracy theory."
@ianbirrell On Feb 19, 2020, the authors of Proximal Origin realized that Jeremy Farrar - who had convened them and led their efforts - had signed the Lancet letter by Daszak condemning all lab #OriginOfCovid as conspiracy theories. Image
Read 5 tweets
Jan 5
5 years ago, the authors of Proximal Origin wondered where the pandemic virus had been transmitting *intensely* so that it gained a furin cleavage site and passed it on.

One said, "No way the selection could occur in the market. Too low a density of mammals." #OriginOfCovid Image
Until today, there has been no reported sign of intense transmission of the virus in animals prior to the detected outbreak in Wuhan.

Investigators, including one Proximal Origin author, searched fur farms in China - no sign of any SARS-like virus.
nature.com/articles/s4158…
On the other hand, a 2018 research proposal surfaced, showing Wuhan and US scientists with a plan to insert novel furin cleavage sites into novel SARS-like viruses.
theintercept.com/2021/09/23/cor…
Read 8 tweets
Jan 1
"5% chance that H5N1 starts a sustained pandemic in humans in the next year. 50% chance that H5N1 starts a sustained pandemic in humans in the next twenty years..."

I invite @slatestarcodex to estimate the chances of a lab-based flu pandemic by 2025!
astralcodexten.com/p/h5n1-much-mo…
@slatestarcodex For consideration, only 4 projects have been flagged by NIH for HHS review since 2017.

One project, funded till 2020, proposed creating ferret transmissible H5N1.

One project, proposed in 2024, was not funded by NIH so no info was made public.
aspr.hhs.gov/S3/Pages/Resea…Image
@slatestarcodex In addition, under the new US gov policy on research that enhances the pandemic potential of pathogens, it will be the funding recipient (not the funder) who is responsible for flagging their own federally funded projects for review.
liebertpub.com/doi/abs/10.108…
Read 5 tweets
Dec 23, 2024
Peter Daszak, who partnered with the Wuhan lab that likely caused the pandemic and is being debarred by HHS, continues to chair @NASEM_Health's forum on microbial threats.

Daszak's forum is hosting @theNASEM workshop on the future emergence of pathogens.
nationalacademies.org/event/43921_01…
@NASEM_Health @theNASEM The event disclaimer and website make no mention of Daszak's involvement in this event or any conflicts of interest. Image
@NASEM_Health @theNASEM This echoes Daszak's behind-the-scenes coordination of the infamous letter in @TheLancet casting lab #OriginOfCovid as a conspiracy theory without disclosing his conflicts of interest.

Read the story about this letter in @theintercept
theintercept.com/2021/09/23/cor…
Read 7 tweets
Dec 22, 2024
In 2020, leading virologists deceived a @nytimes journalist, resulting in NYT dropping the lab leak hypothesis.

Years later, these virologists continue to deny their perfidy while attacking experts like @sigridbratlie who call out their deception.
telegraph.co.uk/us/news/2024/0…
@nytimes @sigridbratlie At the @USFHealth Covid meeting, natural #OriginOfCovid proponents exalted one of these virologists.

Thankfully @ewinsberg read out the slack messages of these virologists which completely contrasted with their public stance.
@nytimes @sigridbratlie @USFHealth @ewinsberg Some consider the lies of leading virologists as indirect evidence for a lab #OriginOfCovid e.g. see the end of this anonymous analysis on youtube.

Why are some smart virologists making so many claims they should know are false?
Read 6 tweets

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