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

Mar 9
I am not 100% convinced Covid came from a lab. I still think there is a small chance the virus emerged in Wuhan without the help of research activities. However, this would mean:

1⃣ The Wuhan-US scientists' entire framework about the spillover risks of SARS-like viruses, building on research and data collected over more than a decade, was incorrect.

2⃣ A highly transmissible, super stealthy virus well adapted for causing uncontrollable outbreaks in multiple animal species left zero trace of its origin in the wildlife or fur farms of China/SE Asia after emerging in only Wuhan out of 1000s of other populous cities.

3⃣ Out of all possible viruses to cause a pandemic and all times for a pandemic to occur, it was an unprecedented SARS-like virus with a novel furin cleavage site, matching the description of a 2018 US-Wuhan research proposal, emerging in Wuhan where scientists worked with such viruses at low biosafety, less than 2 years after said proposal was drafted.

It's not impossible that leading experts were completely mistaken about the exceedingly low odds of such viruses emerging in Wuhan.

It's not impossible that, in 2019, nature churned out a virus matching the scientists' 2018 research plans and that virus emerged in only Wuhan of all places.

But you'd have to be very motivated to believe Covid-19 emerged naturally.
We are unlikely to reach 100% certainty unless a whistleblower appears or the Chinese authorities one day assess that it is in their interest to share the truth.

I am still hopeful that this will happen one day. I believe in human courage.
Before that day, there are several routes of investigation that remain to be explored by the US gov.

Conducting a rigorous, credible investigation of Covid origins can unearth more key evidence while also informing the implementation of new measures to prevent lab pandemics.
Read 5 tweets
Mar 8
Top journals have the power to set global biosafety standards.

It's a problem that they do not see this as their moral responsibility. By publishing & celebrating risky research done at questionable biosafety, they incentivize the 'work fast break things' model of research.
I've given up on journals taking the initiative to be responsible members of the scientific community.

It is up to the U.S. government to tell them to behave responsibly or do business elsewhere.
I would love to be corrected if any top journal can show us that fostering a culture of accountability, scientific integrity, and 'do no harm' is one of their measurable goals as an organization & a strict criteria for decision-making regarding what research/groups to publish.
Read 6 tweets
Mar 2
Dear @NSAGov I've just google searched several human transmissible viruses with the aim of understanding how many are not governed by the Federal Select Agents Program and can be used in gain-of-function research by privately funded groups.

I am not doing anything nefarious 🙏
@NSAGov The answer is there are a lot of human transmissible viruses that are not governed by the Federal Select Agents Program and can be used in gain-of-function research by privately funded groups.
@NSAGov Novel SARS-like and MERS-like viruses are not select agents. Meaning scientists in the US can bring these to their labs in major cities and enhance them without informing the authorities.

At any biosafety level they see fit.
Read 5 tweets
Feb 21
Leading science organizations and journals appear to be utterly tone deaf.

Up till last month, the National Academies kept Peter Daszak of EcoHealth Alliance as head of their forum on microbial threats. Nature journal continues to play the mouthpiece of the Proximal Origin authors & friends.

There appears to be zero introspection that they created/are part of a system that incentivizes risky research including the work in Wuhan that likely caused the pandemic.

Just this month, another top journal published 2 studies where MERS-like viruses were used in human cell infection studies at low biosafety (BSL-2) in Wuhan. The journal did not attach notices of concern to either paper.

Are we just waiting for another outbreak of ambiguous origin to occur? And will we endure more years of "it was the pangolins/bats/raccoon dogs/name your favorite intermediate host?"
@CellCellPress when you publish papers that handle animal pathogens with unclear (human) pandemic potential at low biosafety, you signal to the rest of the scientific community that this is totally fine and will be celebrated in the best scientific journals.
@CellCellPress At the very least, there should be a note of concern. For example, pointing out that the human pathogen MERS coronavirus has a ~30% fatality rate and, in the US, has to be handled at BSL-3. And that researchers should take extra precaution when handling its close relatives.
Read 5 tweets
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

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