The advantage of the RNA vax is their simplicity. They encode only the spike protein because it's the viral protein targeted by most of the antibodies that prevent viral entry. Another way to put it is Abs to the right place on spike are sufficient to block entry. (image Siemens)
The adenovirus vax also encode only spike but express it from Ad. Both types elicit high levels of neutralizing antibodies (nAbs) after just one dose. RNA is better here; in fact 1 dose of RNA gives you similar nAb levels to natural infection.
But immunizing just to spike limits the nAb repertoire. There are only a few places where Abs tend to bind to spike, and it seems binding to a loop containing E484 actually accounts for much neutralizing activity, as E484K drops neutralizing activity 3x.
The delta variant has both E484K to give that 3x lower neutralization, and another mutation P681R that is believed to enhance membrane fusion and thus the rate of viral entry. Overall neutralization activity of antisera is down ~6x (today's Lancet paper)
A landmark paper in May related nAb levels to % efficacy in trials (in terms of % protection from symptomatic disease). Using their efficacy-vs-nAb curve, and with Ab levels at 3x of convalescent sera, the 6x drop in nAb potency predicts efficacy at ~70%. doi.org/10.1038/s41591…
The Chile study I posted above measured nAb levels post-Pfizer/BioNTech at 10x convalescent sera, so it's not clear if 3x or 10x is more common. If 10x, then efficacy would be predicted to remain >85% even with a 6-fold loss of potency against the delta strain.
And now this is rather preliminary and verification is required, but an April preprint reported that nAbs elicited by Covaxin, the whole-killed/inactivated virus vaccine, showed only a 2x dropoff in potency against delta.
That's potentially interesting because whole killed/inactivated virus vaccines present the entire virus. In addition to spike, there are two other surface proteins, E and M. Anti-spike is certainly sufficient for neutralization, but perhaps anti-E and anti-S can contribute too.
So, to wildly speculate: in whole-virus vaccines, maybe you get a mix of the anti-spike (predominantly anti-E484), anti-E, and anti-M. Then if you lose the spike binding with E484K, you still get some neutralizing activity through E and M. Requires more study to know for sure.
The other thing that whole-virus vaccines present are the intracellular viral antigens. Dendritic cells (DCs) route some phagocytosed antigens to MHC-I via cross-presentation, so they can activate CD8 T cells with TCRs that recognize those viral antigens. en.wikipedia.org/wiki/Cross-pre…
Intracellular viral antigens presented on MHC-I by infected cells then induce killing by these activated cytotoxic CD8+ T cells (CTLs). Dogma is that DC cross-presentation is not reliable enough as a vaccine mechanism, but this is not always true. journals.asm.org/doi/full/10.11…
Now whole-virus vaccines such as Coronavac, Sinovac, and Covaxin do seem to have very little activity after the first dose, in contrast to RNA and Ad vaccines. Immune activation is just not as strong with dead virus and adjuvant as RNA or Ad.
However after dose 2, the whole-virus vax appear similar to convalescent sera. If they can maintain 50% neutralizing potency on new variants, then after dose 2, they will still be able to prevent symptoms by >50% and severe cases by >80%.
Adding a correction to main thread: Delta/B.1.617.2 has T478K; Kappa/B.1.617.1 has E484K.
They are on the same loop and both resist neutralizaing antibodies elicited to wild-type spike, so analyses and implications are unchanged.
Also the 2x hit on Covaxin-elicited neutralization mentioned above was with Kappa/B.1.617.1. So for comparison we should look at RNA vaccine-elicited nAbs to B.1.617.1. They are down 7x.
We don't know Covaxin result on B.1.617.2; will be important to get
To add a little background, anti-M antibodies are seen after coronavirus infections. Anti-E antibodies have not been seen so far. nature.com/articles/s4146…
Meant "perhaps anti-E and anti-M can contribute too." Some evidence for anti-M.
In trials the Pfizer/BioNTech vax was estimated to be 88% effective against Delta in UK. That's very good news, and suggests the vax elicits very high nAb levels and/or T cell responses so that the 6x drop in nAb potency is not hindering efficacy too much
3a is another coronavirus transmembrane protein that, in SARSCoV1, was found to be targeted by neutralizing antibodies. It appears nobody has published anything on 3a of SARSCoV2 yet (S is clearly the right protein to target if you have to pick one)
@ScienceTM This paper tells the origin story of nirmatrelvir and ML2006a4 (they are brothers) and reveals why these two drugs work so well.
It also explains the chemical basis for ML2006a4's superior activity, which goes back to a deliberate decision we made back in 2000.
The story began in March 2020 when, entering COVID shutdown, I asked if the hepatitis C virus protease inhibitor boceprevir (BPV, an oral pill) could be adapted for COVID (the viruses are distantly related).
Manually docking BPV into SARSCoV protease suggested yes (Fig. 1A).
So much for viruses evolving to less pathogenicity.
As I've said before, we might expect viruses to become more transmissible, e.g. by replicating faster or suppressing immunity. That's not less pathogenic.
A new report shows recent variants suppress innate immunity more.
There are a lot of plots, but the general gist is that BA.4/5 infection in cells generates less IFN and other innate immunity cytokines than earlier BA.1/2, and BA.4/5 shows less gain from innate immunity suppression by a drug (ruxolinitib) (because it suppressed it already)
Long-time followers recall I had postulated that SARSCoV2 was milder for children was because their innate immunity was better at suppressing viral replication until antibodies were generated.
Actually a person who could have sparked COVID19, accidentally or not, has been ID'ed in the open for a long time.
The name is Zhou Yusen. Evidence? 1. He filed a patent for SARS2 vax in 2/2020, when others only knew of SARS2 from 1/2020 2. He died from a rooftop fall in 5/2020
Those facts are not disputed, but somehow not widely discussed.
The theory isn't mine. It is described in detail by former Assistant Secretary for Preparedness and Response at the US Department of Health, Dr Robert Kadlec, above and more recently below
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.
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.
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.