Alina Chan Profile picture
Feb 15 15 tweets 4 min read
After the first SARS-CoV-2 genome went public, at least 3 separate teams of scientists harnessed 3 different approaches to synthesizing its genome without having to put in any novel cloning or restriction sites. It took each team only a few weeks.
2 of the teams had to put in silent mutations to differentiate the synthetic virus from the natural virus that might've contaminated their lab.

Otherwise how could they know whether the strain they had synthesized was a lab-made virus or a virus from a covid sample?
“Full-genome sequencing showed that the recombinant virus retained the three engineered synonymous mutations with no other sequence changes, demonstrating the rescued virus did not result from contamination by the parental virus isolate​​.”
pubmed.ncbi.nlm.nih.gov/32289263/
"To distinguish our recombinant viruses from the circulating SARS-CoV-2 strains, we introduced a silent mutation (T15102A) into a conserved region in nsp12 to ablate an endogenous SacI site in the molecular clone"
pubmed.ncbi.nlm.nih.gov/32526206/
The other team used a yeast recombination cloning approach.

"Sequencing.. revealed that almost all DNA clones and viruses contained the correct sequence, except for some individual clones that contained mutations.. probably introduced by RT–PCR"
nature.com/articles/s4158…
Seamless cloning of virus genomes has come a long way since the first SARS epidemic 2 decades ago. Back then, scientists had to introduce cloning/restriction sites to make it feasible to clone virus genomes.
For example, to synthesize the 1st SARS virus genome, scientists had to remove + insert restriction sites via silent mutations.

"BglI site at nucleotide position 1577 was removed and new BglI sites were inserted by the introduction of silent mutations"
pnas.org/content/100/22…
When you read these papers on synthesizing virus genomes and introducing novel genetic features to them, there's no rule that your modification must be "in-frame". Basically, whatever helps you to clone the genome and QC it afterwards goes.
It's unclear to me, if one looked at synthetic genetic constructs in the past 5 years, how many insertions/deletions/modifications are in-frame vs out-of-frame.

It depends on the approach the scientist uses and if they rely on specific restriction sites for cloning or QC.
It's possible to ask scientists to get an estimate of how many changes are in- or out-of-frame using public data on synthetic genetic constructs, but more confidence would be gained by looking at each lab's purchases of specific cloning reagents.
An analogy would be like gaining access to someone's grocery receipts to get a better sense of what they might be cooking for dinner.

As opposed to browsing a database of recipes to guess what a particular individual might be most likely to cook.
I likely have also cloned constructs "out-of-frame" or introduced silent mutations several times before. It's not a dealbreaker whether your insertion is in- or out-of-frame. If the cloning produces a functional construct, you choose whichever approach is the most effective.
Some experts are telling people that you can tell from the sequence of SARS-CoV-2 that it's very unlikely to be a lab construct.

How could you estimate the likelihood? Have you got the labs' cloning reagent receipts? Do you know what sequences they had been synthesizing?
We now know, by early 2018, scientists in Wuhan and the US had a pipeline, expertise and everything they needed for synthesizing numerous recombinant SARS-like virus genomes and introducing human-specific novel cleavage sites into the spikes of live viruses for infection studies.
Based on the above knowledge, if you think it is plausible or even likely that SARS-CoV-2 was a lab engineered virus that accidentally reached its pandemic potential and escaped from a lab...

You are not a conspiracy theorist.

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More from @Ayjchan

Feb 14
If a suspect refuses an investigation for 2+ years and then says you should still fully trust whatever evidence they provide years later... is it unfair to say that the evidence provided years later would not be fully reliable?
Are there any investigators who believe that it is appropriate for a suspect to refuse a timely, independent investigation and then later claim that it is immoral to not trust their self-audit?
Apparently some scientists and journalists, who are supposed to have honed their investigative skills over years, believe that the above behavior is acceptable and sufficiently transparent for a matter concerning millions of deaths.
Read 4 tweets
Feb 14
If anyone has actual data, info, screenshots etc. about the missing Wuhan Institute of Virology pathogen sampling database, please send it to a reporter for verification and publication.

If you only have speculation or best guesses about what happened, it will not be helpful.
The archived page above shows that the number of external visits to the database, requests and downloads abruptly dropped to 0 in mid-Sep 2019 and stayed that way.

If anyone is asserting that the database was taken off the public web later than Sep 2019, please show your proof.
For example, what could be considered acceptable evidence is archived versions of the database's public interface after Sep 2019 - showing that users could still visit the database & request data.

Does anyone have this type of evidence or is it all assertions without evidence?
Read 6 tweets
Feb 14
This is an archived page of the Wuhan Institute of Virology 野生动物携带病毒病原特色数据库 database backend h/t @C_Small_

It lists the date, # independent IPs, # visitors, page visits, # requests, and downloads (GB). These ground to a halt in Sep 2019.
archive.md/9MNVZ
@C_Small_ Interestingly, the database interface page was visited from outside of China as well during this period:
Unfortunately, because the database's public interface page has been removed, it's not easy to tell what was originally there.

A public description of the interface had been archived:
archive.fo/jPPkB
Read 11 tweets
Feb 13
People on both sides of #OriginOfCovid agree it was risky to experiment with live SARS-like viruses at BSL2 (low biosafety) & virus hunting + manipulation possibly led to COVID.

The key difference is that one side doesn't think the lab has been transparent. The other side does.
This is why one side insists that there should be an inspection of lab records, research documents, databases etc.

Whereas the other side is willing to take it on trust that the Wuhan lab(s) did not have a SARS-CoV-2 precursor in their possession prior to the detected outbreak.
As a scientist, I am incredulous that all of the virus strains and sequences in a top research lab have already been published at any one time.

But some other scientists seem to believe it is possible for all virus strains and sequences in a lab to be in the public domain.
Read 13 tweets
Feb 12
I'm proud of VIRAL. @mattwridley & I had to write this book in record time, compiling months of research and fact checking the book multiple times.

Despite great efforts by natural origin proponents, they have failed to point out even a single piece of misinformation in VIRAL.
@mattwridley The largest criticisms have been that VIRAL is too technical for some readers and that it does not conclude whether SARS-CoV-2 / COVID-19 emerged naturally or due to research activities.

We can't do anything about the latter because there is no direct evidence for either origin.
One question that often comes up is how can we investigate now that 2 years has passed? Isn't this a situation where we will never know the #OriginOfCovid?

My answer is no, there are so many approaches of investigation still left unexplored. It's way too early to give up.
Read 9 tweets
Feb 9
2 early takeaways from this saga:

1. Chinese scientists asked @NIH NCBI database to delete deposited data containing sequences of early versions of SARS-CoV-2 virus.

2. US-based @biorxivpreprint blocked European scientists from posting their analysis of this data as a preprint.
Never thought I'd ask this, but... @biorxivpreprint @cshperspectives

What is bioRxiv's gatekeeping policy when it comes to original analyses? And would you consider a more transparent approach to this gatekeeping by publishing the name of the reviewer and reason for rejection?
@biorxivpreprint @cshperspectives Although bioRxiv is not a peer review service, it still confers a certain level of credibility to the preprints it has screened.

Has the team at bioRxiv considered that now there may be conflicts of interest among its screeners that should be carefully managed?
Read 5 tweets

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