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I can understand how previous infection can confer immunity, especially since the immune response is built against live virus, not just spike protein.

What I don’t understand is how vaccination and boosting using an mRNA vaccine that contains only spike protein from the original SARS2, and which is almost completely evaded by the BA.4 and BA.5 variants, can confer protection against severe illnesses caused by those variants.

What is the biochemical process that provides that protection?

EDIT: Is this protection just a happy mantra, or is it actually that there is no protection against the new variants, but the intensity of the disease from them is far less than from the original variant (and our treatment is getting better)?

One theory I have heard to explain this is that the vaccine is simply suppressing immune response, which helps prevent the cytokine storm that led to severe disease. Of course, this might also make infection more likely, which may explain why so many governments have stopped publishing the case rate breakdowns by vax status.

It makes a kind of intuitive sense: if you make your own body produce some key portion of the virus, maybe your immune system gets tricked into thinking it's not such a big issue?

> the vaccine is simply suppressing immune response, which helps prevent the cytokine storm that led to severe disease.

"Response" is many different things. The vaccine boosts response b/c you have antibodies, so it's much less likely that your body has to do a hail mary las ditch (cytok storm).

> why so many governments have stopped publishing the case rate breakdowns by vax status.

But there's enough data out there to have a clear picture: vaccines or previous infections won't protect you from being infected by the recent strains (BA.2.75, BA.5, etc) but will protect you from severe disease or dying. Maybe it can be improved by nasal vaccines (what happened to those?) but who knows...

> It makes a kind of intuitive sense: if you make your own body produce some key portion of the virus, maybe your immune system gets tricked into thinking it's not such a big issue?

This one is completely off the mark. For starters, not all vaccines have your "body produce part of the virus", yet all help to prevent severe cases and death.

There is protection against the new variants. The human immune system has different levels of protection, and these mRNA vaccines seem particularly effective at triggering one of the most flexible, long-term forms -- cellular immunity.

At a very high level, this is the explanation: the spike protein in Omicron has many differences from the vaccine strain spike, but it's still largely the same protein. The immune system is chopping up the protein into chunks, and T- and B-Cells are specializing to recognize those chunks. This kind of immune response (the "cellular immune response") is slower to ramp up than the antibody response that many people have fixated on, but it's a much more robust defense mechanism; B- and T-Cells are very good at providing generalized antigen recognition. There have been at least 2-3 papers I'm aware of where labs have directly demonstrated that vaccinated people are producing robust immune responses to Omicron proteins.

I'd have to dig these up again, and they're not exactly comprehensible by non-specialists, but the executive summary is that we have laboratory and clinical and epidemiological data that the vaccines are still very effective against severe disease.

What the vaccines don't do anymore, is protect against infection. That was probably never a realistic goal for a respiratory virus, but it's definitely not practical with a vaccine that produces antibodies that target a very old spike protein.

If you have a link, I’d be interested in reading the paper!

Here's one from Cell -- as I said, it's very technical, but the TL;DR is that 84% of CD4+ and 85% of CD8+ memory T cell responses to the Omicron spike protein are preserved, compared to an average of 90% and 87% respectively for the other variants:

https://www.sciencedirect.com/science/article/pii/S009286742...

Here's another:

https://www.nature.com/articles/s41586-022-04460-3

> Between 70% and 80% of the CD4+ and CD8+ T cell response to spike was maintained across study groups. Moreover, the magnitude of Omicron cross-reactive T cells was similar for Beta (B.1.351) and Delta (B.1.617.2) variants, despite Omicron harbouring considerably more mutations. In patients who were hospitalized with Omicron infections (n = 19), there were comparable T cell responses to ancestral spike, nucleocapsid and membrane proteins to those in patients hospitalized in previous waves dominated by the ancestral, Beta or Delta variants (n = 49). Thus, despite extensive mutations and reduced susceptibility to neutralizing antibodies of Omicron, the majority of T cell responses induced by vaccination or infection cross-recognize the variant.

I may have read a third, but I can't find it easily, and these two should be more than enough to back up what I wrote / get you started.

Symptomatic infection is not the point of vaccination. The important bit is this: “Previous infection alone, BNT162b2 vaccination alone, and hybrid immunity all showed strong effectiveness (>70%) against severe, critical, or fatal Covid-19 due to BA.2 infection.” Though they didn’t list actual percentages, other studies showed vaccination provided ~90% reduction in deaths.

That said there are conflicting studies: “This report details the findings of a case-control evaluation of the association between vaccination and SARS-CoV-2 reinfection in Kentucky during May–June 2021 among persons previously infected with SARS-CoV-2 in 2020. Kentucky residents who were not vaccinated had 2.34 times the odds of reinfection compared with those who were fully vaccinated (odds ratio [OR] = 2.34; 95% confidence interval [CI] = 1.58–3.47).” https://www.cdc.gov/mmwr/volumes/70/wr/mm7032e1.htm?s_cid=mm...

The nuances are complicated. False positives are a real concern for people avoiding vaccination. People that survive the first infection without vaccination are a meaningfully different population than the vaccinated population. Similarly people that get vaccinated after infection have received vaccination more recently etc.

That MMWR study was a pile of flaming garbage. First, it was conducted in May 2021 (before the Delta wave) so everyone who was vaccinated was well within the first few months of their second dose. We now know that protection against infection rapidly fell after about 4 months.

But also, it was just methodologically flawed -- they didn't bother to correct for the bias that people who were vaccinated after infection in early 2021 were probably behaving differently than those who had not been vaccinated at that time.

If you're going to cite an old MMWR article as "evidence" against the now overwhelming pile of papers demonstrating that the immune system works pretty much as we expect from immmunology 101, don't forget that in early 2022 they released this much better, much larger (N=1.1M people) cohort study, which dramatically showed the opposite of what you're claiming. Prior infection obviously provided robust protection against Delta, on par with the vaccines:

https://www.cdc.gov/mmwr/volumes/71/wr/pdfs/mm7104e1-H.pdf

> the immune system [still] works pretty much as we expect from immunology 101

Shocker. Why did we have to learn this again? How were the policies that diverged from the immunology 101-based position justified? This should be our starting point and we should not base policies on the opposite conclusion without good evidence to the contrary.

The question isn’t if catching COVID provides some level of protection, the question is if people who have gotten COVID should also get vaccinated.

Saying a study is garbage when you disagree with the results is not how evidence based medicine works. Unless there was actual fraud or gross incompetence, every study should provide something of value.

Hypothetically, if vaccination provides enhanced short term protection for people after catching COVID which also provides short term protection then recommending waiting X months after getting COVID to get vaccinated is one option. Alternatively, if post COVID vaccination did absolutely nothing then you could recommend skipping it, ignoring false positives.

The study was garbage not because I personally disagree with the results, but because of the reasons I stated:

1) in retrospect it was obviously incorrect, and

2) even at the time, a reasonable scientist could have concluded that it was flawed

I don't generally call papers "flaming garbage", but some are so egregiously, transparently awful -- at the time of publication -- that saying otherwise is dishonest. That MMWR study was one.

“But also, it was just methodologically flawed -- they didn't bother to correct for the bias that people who were vaccinated after infection in early 2021 were probably behaving differently than those who had not been vaccinated at that time.”

Your only complaint relevant at the time of publication was people that where vaccinated acted differently, that’s also true of the study you linked. It wasn’t double blinded making it “hot garbage” by your logic. Presumably the only reason you linked it was it didn’t contradict your assumptions, even though it failed to address the actual question of how useful post COVID vaccination is.

Except we care about real world outcomes so a double blind study would be less relevant making your original complaint pointless.

What's odd is how many people ignored, denied or actively resisted the idea of natural infection conferring immunity.

And at the same time supported severe covid restrictions until a vaccine is available. The paradox of course is that the likelihood of there being an efficient vaccine is very low if you don’t develop immunity naturally.

> the likelihood of there being an efficient vaccine is very low if you don’t develop immunity naturally

where did you read this?

The way traditional vaccines work is by injecting an attenuated virus and letting the natural immunity do the rest. If natural immunity doesn’t work on the original virus, it is unlikely it will work on the attenuated virus.

what does that have to do with the restrictions? the logical corollary to your statement seems to be, if the body IS capable of natural immunity, then it is likely that it will work on the attenuated virus (provided it's not too attenuated, maybe)

That isn't it at all, the question isn't "does natural immunity happen", but "what's the overall population cost of natural immunity".

Long covid, and greater impact on certain individuals were well known by that point. Just saying "let 'er rip, go natural immunity" isn't the responsible move. Perhaps you're ok with the risks for you, but faulting a health officer for taking a different more conservative position is hardly a reasonable opinion.

> Long covid, and greater impact on certain individuals were well known by that point.

"Long covid" is not defined. There is no test. There is no objective signature. Literally anyone can claim that they have it, and not be wrong. I'm not saying it doesn't exist, but I'm telling you that we have no idea how prevalent "it" is, and we don't have any idea how "it" compares to the consequences of other common respiratory illnesses. We've simply never bothered to look, and uncontrolled studies where someone enumerates a long list of things that happened after Covid, in a large group of people, are not evidence of those things being caused by Covid.

Said differently: if you have a nearly ubiquitous illness, how can you say anything about causality regarding anything that follows?

So what we have here is a pile of questionable research, a large group of people who are scared and demanding that action be taken, and politicians who are more than willing to "take action" by pushing aside, censoring, and otherwise bullying the scientists who stand in the way of their actions.

>I'm not saying it doesn't exist

okay, well, others with relevant qualifications are saying it DOES exist, so since nobody seems to be saying it doesn't, I guess we can go with their expert conclusions.

The point of the article is that people with relevant qualifications are saying things like that, whilst also saying in private "this is wrong but I just need to get to retirement".

Pretty much anything public health people say on the topic of COVID turns out to be wrong on close inspection. It's really astounding. Even very basic things like getting an actual clinical definition of COVID itself (let alone long COVID) turns out to be impossible, which is why the official definition governments use is "got a positive on a COVID test". That's not actually a disease symptom but COVID isn't defined by symptoms any more than long COVID is.

The reason this happens is that public health is an authoritarian collectivist concept - the government will make decisions for the collective good even if individuals must suffer as a consequence. The entire culture of that space is dominated by a mindset that says, "we will obtain compliance by making scientific sounding claims, because people respect science and will follow it". That's why COVID research is so full of conflicting and nonsensical claims.

> That isn't it at all, the question isn't "does natural immunity happen", but "what's the overall population cost of natural immunity".

Do you think we all have the memory of goldfish? In the height of the pandemic people were saying natural immunity was insufficient to prevent further infection to the degree that would matter the few who were talking about the "cost of natural immunity" (or any other sort of level headed adult discussion about tradeoffs) were ridiculed as enabling the anti-vaxers.

>Perhaps you're ok with the risks for you, but faulting a health officer for taking a different more conservative position is hardly a reasonable opinion.

This is a two way street. If you get to be conservative about natural immunity the other guys get to be conservative about the vax.

There has been an alarming pattern of public health communication throughout the pandemic: public official (Fauci, WHO official, CDC Director, President, Governor, etc.) makes assertion A about COVID, questioning of assertion A is harshly criticized as anti-science, racist, right wing, wanting to kill grandma . . . Six to twelve months later, the same public health establishment admits not only was assertion A not true, but it was never believed by said establishment.

Most blatant examples:

- Masks are not protective

- The vaccine prevents infection (entire basis for mandates)

- There is no evidence for lab leak

- Natural immunity is not as effective as vaccine immunity

- the virus is not spread via aerosols

It's more like while you're obtaining "natural immunity", you're shedding virus that infects others. Similarly with masks, they weakly protect you from others, they strongly protect others from you.

I feel like everywhere I look in the anti-COVID-vax community, no one reckons with the fact that their position gets others sick, and those people might die. Even this article focuses strongly on children not needing masks or vaccines, mentioning not at all kids getting others sick.

Some cites:

https://pubmed.ncbi.nlm.nih.gov/33721405/

https://hms.harvard.edu/news/children-spread-covid-19

https://ufhealth.org/news/2021/uf-study-sheds-light-roles-ch...

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7156154/

> The protective effect of prior infection is not uncertain, nor is it changing.

The paper you linked shows effectiveness of previous infection alone at 46%, 3 vaccine doses at 52% (and slightly above the upper end of the confidence interval for infection only), and previous infection and 3 doses at 77%. When I looked for earlier studies, the first one that popped up was this one from Sept 2021, which finds that previous infection gives a 90% reduced risk re-infection.

This seems to be consistent with what has been reported more popularly; in 2020-2021 it seemed that the immune benefit from a previous infection could last several months, and that this informed the timing on when boosters were recommended. Whereas now it seems it's significantly easier to be re-infected with an omicron variant relatively soon after a previous infection.

The finding of 90% in late 2021 vs <50% now does sound like the protective effect of prior infection _is_ changing.

You're quoting numbers concerning protection against symptomatic infection. While perhaps scientifically interesting, this is irrelevant. You are going to get Covid multiple times in your life, regardless of your vaccination or infection status.

Look a Figures 1, 2 and 4, and you'll see clearly that protection against severe disease remains quite robust. Protection against severe, critical or fatal Covid-19 due to any Omicron infection is shown at 91% (95% CI 60-100) after prior infection (Figure 2D).

https://www.nejm.org/doi/full/10.1056/NEJMoa2203965

Why is protection against symptomatic infection not relevant? Because the bar for "severe" is set rather high, there's plenty of room for symptomatic illness to be personally, economically, and systematically damaging without being "severe", and I think a lot of people find that waning protection to be quite relevant.

> You are going to get Covid multiple times in your life, regardless of your vaccination or infection status.

Yeah but whether you expect to get it once every couple years or multiple times a year is meaningful to what living in a post-covid world looks like.

Earlier your very firm statement did not qualify the unchanged protective effect as being limited to severe, critical or fatal disease, and I think you're moving goalposts.

> The protective effect of prior infection is not uncertain, nor is it changing.

If you're going to quote me, quote me -- don't paraphrase me and leave out essential context. Here is what I wrote:

> The protective effect of prior infection is not uncertain, nor is it changing. There have been dozens of papers now, all saying the same thing: natural infection is at least as protective (if not more so) than even 3 doses of the current vaccines.

I was saying that natural infection is equivalent to vaccination -- if not better. Then, in the same comment, I explicitly said that none of this will prevent re-infection:

> Norway is saying what it is, because we know that most people -- vaccinated or previously infected -- will eventually get re-infected. But even if you are re-infected, you will be well-protected against severe illness.

Did people originally overstate the claim that vaccination would prevent infection? Absolutely. Do we now know this to be untrue? Again, absolutely. You're going to be re-infected multiple times in your life. Cannot be helped.

But it's still true that infection and vaccination offer at least equivalent levels of protection. So if you're concerned about the protection of "natural immunity" -- by whatever standard -- then I have bad news for you: the vaccines are no better.

> natural infection is at least as protective (if not more so) than even 3 doses of the current vaccines.

This claim is directly contradicted in the paper you linked:

> The effectiveness of previous infection alone against symptomatic BA.2 infection was 46.1% (95% confidence interval [CI], 39.5 to 51.9).

...

> The effectiveness of three doses of BNT162b2 and no previous infection was 52.2% (95% CI, 48.1 to 55.9).

Those confidence intervals overlap. You're cherry picking one plot, for one outcome, for one vaccine, out of the entire paper, and it's not refuting the conclusion of the paper.

if they overlap, how do you support your statement that the opposite is true?

"natural infection is at least as protective (if not more so) than even 3 doses of the current vaccines."

GP is citing a part of the paper where they show...that natural infection is statistically indistinguishable from 3 doses. QED.