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

Apr 22
Those dismissing a lab #OriginOfCovid have had to make numerous concessions over the past 4 years.

We now know Wuhan scientists conducted risky experiments with novel SARS-like viruses at low biosafety & planned in 2018 to create viruses with the traits of the Covid-19 virus.
We also know the data on early cases & Huanan market shared by Chinese scientists do not shed light on #OriginOfCovid

Proponents of natural origin continue to argue that it is the totality of evidence that supports their hypothesis but this could be said for lab origin as well.
The latest defense for a natural #OriginOfCovid is that, if a lab leak had occurred, the Wuhan scientists would have acted all suspicious and essentially given the game away, thereby putting themselves, their colleagues & their families in immediate and deadly peril.
Read 8 tweets
Apr 18
Freedom of speech is important in academia & science but difficult to navigate when it comes to politicized topics.

With #OriginOfCovid, some scientists, journals & reporters have competing interests & may be blamed if research they conducted, funded or glorified caused Covid.
On Tuesday’s hearing, chief editor of Science said the scientific community contributed to politicization of Covid & it was wrong to paint 'lab leak' as a conspiracy theory.

There was widespread consensus, Democrat or Republican, that #OriginOfCovid remains unresolved.
Several representatives asked for forward-facing solutions but none were presented. Today, the media continues to hang onto mistakes & politics of the past.

When confronted, many scientists or journalists who misled their peers & the public on #OriginOfCovid make no apologies.
Read 10 tweets
Apr 11
The @BulletinAtomic Pathogens Project successfully unified experts from opposing ends of #OriginOfCovid, representing diverse disciplines & cultures.

The outcome was a set of practical and high impact recommendations that policymakers are taking note of.
thebulletin.org/2024/04/how-to…
@BulletinAtomic Please see this thread for highlights from the report:
@BulletinAtomic The point of assembling an international task force of experts with truly different view points on #OriginOfCovid and what qualifies as risky research was so that the consensus recommendations would be robust to attacks from angry people on both sides of this issue.
Read 12 tweets
Apr 11
Leaders of scientific funding agencies said Proximal Origin was a nice job. According to the lead author of Proximal Origin, Farrar, Fauci & Collins had advised and led them as they wrote the letter.

So why won't @NatureMedicine put these leaders in the acknowledgements?
Image
The only scientist acknowledged in Proximal Origin arguably contributed much less than these 3 leaders.

He wasn't even at the Feb 1 meeting organized by Farrar where #OriginOfCovid was hotly debated and Proximal Origin was initiated.
Beyond what @Bryce_Nickels pointed out in his letter to @NatureMedicine & International Committee of Medical Journal Editors, the Proximal Origin authors failed to point out that their funder(s) had been involved in the work.
nature.com/nature-portfol…

Image
Image
Read 7 tweets
Mar 19
Serious question:
Is it acceptable for scientists to publish assertions that they know are not well supported by the available evidence?
The first author told Nature they really, really wish they could refute a lab origin but it's just not possible given the data. They were rejected.

They then went to Nature Medicine, telling the editor they would make clear that #OriginOfCovid is natural.
After Proximal Origin is published, the first author continues to worry about lab #OriginOfCovid - citing "definitely concerning work" at the Wuhan Institute of Virology. Image
Read 7 tweets
Mar 18
What I think would be accurate reporting

2020: Some 🧑‍🔬 dismissed lab #OriginOfCovid as implausible/conspiracy theory. Journalists captured. Issue polarized. Mudslinging from both sides.

2021-: FOIA/subpoenas show 🧑‍🔬 went too far, misled journalists. Lab origin plausible/likely.
2024: Some 🧑‍🔬, including those who misled journalists on #OriginOfCovid and engaged in their own repeated harassment of scientists asking for fair investigation, complain to employers about harassment by scientists on side of lab leak.
Even scientists who acted completely professionally and civilly have been silenced on lab #OriginOfCovid and advocating for better biosafety to protect millions or billions of lives from lab-based pandemics.
Read 5 tweets

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