The full DEFUSE proposal on gain-of-function experiments on bat coronaviruses is available, and I'd say it's quite shocking. It does not lay out a plan to create SARSCoV2, but does propose to identify and culture natural sarbecoviruses with the ability to infect human cells. A 🧵
There are threads interpreting the DEFUSE proposal as intending on making SARSCoV2. A careful read shows that is not the case. However the intention was to identify natural viruses with features that would help them infect cells. So it may be not much of a difference functionally
The draft proposal and related documents can be downloaded at the link below. We know DARPA rejected the final submitted proposal for being too risky. This draft proposal certainly matches that description. Were the experiments attempted? We don't know.
I'll jump right to it. Page 518 in the downloaded PDF proposes to sequence wild sarbecovirus "strains" for spike (S) genes, then insert them into the genomes of WIV16 and SCH014, two sarbecoviruses deemed less pathogenic than SARSCoV1 (by Shi Zhengli, who had isolated them).
The subset of "chimeric viruses that encode novel S genes with prepandemic potential" (WIV16 or SCH014 backbone, new S) will be identified based on better replication in human cells or in mice expressing human ACE2. Recall the S genes came from natural strains that were sequenced
The natural strains that provided S genes conferring better replication in human cells will then be rescued. They will be fully sequenced, the sequences grouped into 95%-similar subspecies, and a consensus sequence identified (unclear if an average or "representative" sequence)
The consensus genome for each interesting variant will be synthesized in 6 pieces then stitched together using restriction sites that do not disturb the coding sequence (presumably they mean can disturb the RNA but not the peptide sequence), and real live viruses recovered.
Finally they will see how bad these isolates of wild sarbecovirus variants with spike proteins that aid infection of human cells really are, in human cells and hACE2 mice again.
That does sound like a recipe for potential disaster in any place other than a BSL4 facility.
The proposal explains how you can isolate a virus with an unusual spike feature (the FCS) without deliberately engineering it in. Essentially it proposes to set up a genetic screen to find those rare performance-enhancing spike proteins, then grow up that unusual virus.
This proposal also demonstrates by counterexample why engineering a FCS into a viral backbone without published characteristics never made sense. It only makes sense to engineer changes into a well studied less pathogenic virus, such as WIV16 or SHC014, exactly as proposed here.
That's why I leaned against SARSCoV2 being engineered (as I told @zeynep below). But the DEFUSE proposal now raises another way to obtain the unusual features of SARSCoV2: not by direct engineering, but by screening and amplification of natural strains.
It's all very strange though. The behavior of Shi's team in the early days (taking photos in a restaurant after working hard in the lab, musing with friends about where it came from) isn't what you'd expect from someone with consciousness of guilt. Yet the circumstances align.
And recall that the US IC believed that the Chinese didn't know and don't want to know. I still think it's possible that an unknown SARSCoV2 jumped out of a bag of bat feces (still a research incident). Yet DEFUSE does seem eerily predictive. Mysteries...
BTW some believe a subsequent part of the proposal to fix broken protease sites is damning by explaining how a furin cleavage site appears in SARSCoV2 and not other sarbecoviruses. However I am not sure that SARSCoV2 would have come from this work if that fix were necessary
The sentence in question is "where clear mismatches occur in these S2 proteolytic cleavage sites of SARSr-CoV, we will introduce the appropriate human-specific cleavage sites". This sentence is lousily written; should have been "where latent cleavage sites may exist, we will..."
and the word "these S2 sites" should be better defined. AFAICT "these S2 sites" most likely refers to potentially latent sites for all proteases previously mentioned as processing S2, trypsin, cathepsin, TMPRSS, or furin.
So indeed a FCS could have been artificially introduced via this process, but then, if that's what happened, recall it means the researchers would have needed to have identified the SARSCoV2 precursor without a FCS as having a more effective spike protein in the previous step
So for the FCS to have been introduced into a newly cloned strain, a SARSCoV2 precursor would have needed to have passed the selection for better spikes in order to have been a newly cloned strain to begin with. I wonder if this is true?
Maybe someone more familiar with SARS2 spike can tell us if SARS2 spike minus the FCS is already capable of mediating improved human cell entry compared to WIV16 or SHC014 spike
Could someone have cloned some new sarbecoviruses without going through the first selection and created cleavage sites on their S proteins without first (1) publishing the baseline natural characteristics of those viruses, or (2) testing the effects in chimeric WIV16 or SHC014?
It's possible, but that seems like a lot to do without publishing or publicizing in the interim. So possible but also possibly not. Again the proposal is eerily predictive but not all the human behavioral factors fit. One must be careful of selective posthoc mental fitting.
Nevertheless the DEFUSE proposal proves that everyone involved in coronavirus research knows that a lab leak is a plausible hypothesis. We already knew that from logical priors and from Zhengli Shi's responses to SciAm and Science.
What DEFUSE additionally proves is that some of those most vehemently denying the possibility of SARS-CoV-2 originating from a lab leak are among the most aware of its plausibility. Ironically they are in the US, where public opinion has to be shaped and can't simply be dictated.
For chimerogenesis and viral genome assembly, UNC (Baric) is listed as primary responsibility, but Shi's lab at WIV had performed those techniques before, so had the ability to do the work using other funds if they wanted to.
Anyway the general point is that someone proposing to find or make viruses that fit the SARS-CoV-2 description doesn't prove that they did it. But it does soundly refute denials, by the proposers and those blindly echoing them, that it was a ridiculous or impossible idea.
IgG3 antibodies bind Fc receptors on phagocytic cells like macrophages so that viral particles bound to them will be ingested and destroyed. This antibody-dependent phagocytosis (ADP) is a crucial part of the immune response to viruses...
because just one bound IgG3 molecule on a virion lead to its destruction, whereas multiple bound IgG molecules would be needed to block entry (due to multiple S proteins per virion). Also you need to clear circulating viruses to stop spread; killing infected cells is too slow.
In 2023 about 70,000 Americans died of SARSCoV2, although >95% have some immunity. That's about 2x the usual annual deaths attributed to flu.
In people with immunity, SARSCoV2 has an infection fatality rate similar to flu, but it's much more contagious and widespread.
We spent years of effort trying to eke out small decreases in flu fatality. COVID19 has undone that and more, with >1M deaths in 3 years and now a higher hospitalization and fatality burden than flu.
Widespread annual boosting is more important for reducing death for SARSCoV2 than flu, because of its high contagiousness.
Unfortunately SARS2 booster uptake is even lower than flu or RSV.
Even more impressively, Novavax did it as a company on the edge of bankruptcy. That means FDA staffers aren't going to treat its applications with kids gloves (they didn't), because they aren't sure there's a high-paying job at Novavax awaiting them
If it wasn't obvious before, that makes Novavax a national treasure, but unfortunately mismanaged by the board in not installing a competent CEO and manufacturing directors when they needed to scale up.
Pretty much as I wrote here, the week molnupiravir was approved, in December 2021: "A new drug to treat covid could create a breeding ground for mutant viruses"
By understanding mechanism, you can predict these things, 2 year before data can prove it.
More from today's Nature news: "The identification of transmissible viruses with clusters of mutations that resemble those expected to be induced by molnupiravir is a clear warning that some of the mutations caused by this drug are not as lethal to the virus as intended"
24h after my Novavax COVID shot (and flu shot), and very happy. Much milder side effects than my 5 earlier COVID vaccines.
It's just my experience of course, but I'm hopeful we may finally have a sustainable and acceptable format for annual vaccinations.
A short 🧵
Earlier COVID19 vax were 4 Pfizer original and 1 Moderna bivalent, plus a BA.5 infection in 2022 summer 3 weeks after #4.
All RNA vax shots produced noticeable side effects of fatigue and/or headache within 24h.
This time no fatigue or headache after Novavax and flu.
Flu and Novavax shots went into different arms. There's mild tenderness, similar both arms, but only if I press.
The needles were probably big (I didn't look) as there was a big blood spot on each band-aid. So basically the pain is about what you'd expect after being pricked.
Missed this excellent commentary calling for FDA to share all data on Paxlovid. FDA gave it full approval based on the one trial in nonimmune patients (now irrelevant) while another trial in immune patients (relevant) trended to but did not meet endpoints. medpagetoday.com/opinion/second…
Meanwhile Pfizer had run more trials but didn't reveal the data.
As small companies know, FDA usually requires 2 out of 2 positive trials to approve, and indications are restricted to populations mimicking the trials. If only 1 out of 2 meet endpoints, they are required to do a 3rd.
Pfizer had 0 out of 1 successes in the immune population.