Full vaccination suppresses SARS-CoV-2 delta variant mutation frequency | Hacker News Reader

Full vaccination suppresses SARS-CoV-2 delta variant mutation frequency

medrxiv.org

49 pointsrbanffy25 comments

We conclude that the virus becomes more contagious as it is screened through the vaccinated population and the resultant strain becomes the dominant strain and able to infect the entire population.

We recommend that: 1) universal vaccination should be administered as soon as possible to suppress the generation of virulent mutations;

Wait, I’m being punked.. right?

How is universal vaccination the solution, if it is literally the cause of the more contagious strain?

The logic is a bit circular, no?

> The logic is a bit circular, no?

Yeah the paper is littered with these kinds of gaps in reasoning, see my other comment for a more detailed critique.

Universal vaccination is how you kill it completely, like we did with smallpox and almost did with polio.

Nope. The virus can already spread among vaccinated.

No, not all of them

The OP alleges it can't sufficiently mutate among the vaccinated, so their recommendation of full vaccination to eliminate the virus is perfectly consistent. Opening up and letting everyone get delta, vaccinated or not, is going to happen sooner and is not good because passing through the unvaccinated will cause many new mutations some of which might start new waves.

That's not at all what the paper says.

>The OP alleges it can't sufficiently mutate among the vaccinated, so their recommendation of full vaccination to eliminate the virus is perfectly consistent.

From the study:

"We conclude that the virus becomes more contagious as it is screened through the vaccinated population and the resultant strain becomes the dominant strain and able to infect the entire population."

The main takeaway from the paper is that the vaccinated are driving new variants.

>Opening up and letting everyone get delta, vaccinated or not, is going to happen sooner and is not good because passing through the unvaccinated will cause many new mutations some of which might start new waves.

Again, the paper states the vaccinated are driving new mutations. Technically due to natural immunity, the unvaccinated who have been previously infected are now in a better position than the vaccinated. They don't contract, get sick or spread whereas the vaccinated do. The big exception is unvaccinated who have never been infected by this coronavirus or any other past coronavirus. They are still susceptible to infection, spread, etc.

> The main takeaway from the paper is that the vaccinated are driving new variants.

Filtering is the takeaway, one dominant strain and orders of magnitude less variations since most variation is not viable in a vaccinated public.

If we have a highly variable virus that never goes away. That is the flu.

This is next level as neither of those had animal reservoirs.

On Polio "The fact that the virus can only survive in humans (and no other animals) makes it possible to completely eradicate the disease from the world – if it was a virus with an animal host such as influenza (birds) or tuberculosis (cows) that occasionally mutates to attack humans, polio could only ever be controlled but not eradicated."

Covid transmits in animals. CDC says based on current data, transmission to human is low (but not impossible) but more studies are needed. The fact they can get it is already not on the same scale as smallpox or polio.

https://www.cdc.gov/coronavirus/2019-ncov/daily-life-coping/...

In what way did vaccines directly cause the virus to mutate to the Delta variant?

It seems counterintuitive at first, but the logic is sound. More infections = more mutations. More time = more mutations. By having a significant proportion of unvaccinated people keeping the pandemic going, juxtaposed with a large, maybe even majority of people vaccinated, it confers an evolutionary advantage to any mutation that crosses from unvaccinated to vaccinated. A rapid increase in vaccination is needed to stamp out the infection before it can mutate. A slow burn is a worst case scenario, as it just keeps the door open for the shit to keep escaping.

The vaccinated shed mutations - it’s the conclusion of the paper. They are the petri dishes of which new vaccine derived mutations spawn.

You’re attempting to tie these mutations to only the unvaccinated. They likely shed mutations as well but that’s not what this paper highlights.

Not only can the vaccinated spread the virus but they’re likely making it more pathogenic in the process. See here:

https://journals.plos.org/plosbiology/article/info:doi/10.13...

Not sure why this is getting so many upvotes - the title would be good news to hear, but perhaps not many have been able to review the paper thoroughly.

This is a relatively low quality paper that presents very tenuous supporting evidence of it's claims & conclusions.

There is no randomization, placebo-control, or blinding - nor any serious consideration or analysis of confounding factors such as natural immunity, comorbidities, and other demographic biases. Evidence that doesn't fit their hypothesis (eg Australia) is dismissed with barely a hand wave. The P-values & correlation coefficients are borderline statistically insignificant, the citations are comically sparse, and the conclusions lack a critical & balanced evaluation with respect to the existing literature.

We shall see if the paper passes any legitimate peer review - I'd bet against it.

Quoting from OP:

> we first analyzed the correlation between the rates of full vaccination and the point mutation frequency (Mf) of COVID-19 delta variants’ genome in 20 countries

> Complete SARS-CoV-2 genome sequences with high coverage from June 20 to July 3 2021 in 20 countries were collected from the Global Initiative on Sharing All Influenza Data (GISAID)

> We found that Mf was logarithmically reduced as the full vaccination rate increased in 16 of the 20 countries (R2=0.878, Figure 1A)

> With 10.8% vaccinated rate, Mf was exceptionally low in Australia, likely as a result of the national lockdown restrictions.

> In contrast, Mf is higher in Japan, Switzerland, and United States, suggesting that their mitigation strategies have been less successful

> We chronologically analyzed SARS-CoV-2 delta variant sequences in the UK (N=27,344), India (N=4,451) and Australia (N=305) from 13 February to 3 July 2021, respectively in the GISAID

> Genome alignments and analysis using the Tajima D test, a neutrality statistic widely used in population genetics, were carried out

> The Tajima D test (D’) compares pairwise nucleotide diversity (π, the average number of nucleotide differences per site between two sequences) and total polymorphism to infer selection and demographic events

> We observed that π was significantly lower in the UK (π< 1.5 × 10−4) than others which emerged after April 24, 2021 (π> 2.0 × 10−4; p<0.01)

> we recommend that: 1) universal vaccination should be administered as soon as possible to suppress the generation of deadly mutations

“mitigations strategies such as personal protection equipment, social distancing, etc., should continue to be employed to prevent viral transmission until the virus is eradicated”

I’m sorry to say, but its not ever going be eradicated, especially with vaccines that don’t stop you getting the virus, or transmitting it.

"Social distancing should be employed until the end of time" is totally unsustainable. Technically speaking it means the end of casual sex.

not at all advocating for this but this may reduce HPV and STIs..

In addition to that this can't go the way of smallpox because covid has animal reservoirs. Smallpox did not so we could eliminate it. Vaccine or no, we've known since the beginning that eradicating this virus was nigh impossible.

"It is still unknown whether COVID-19 Variants are evolving randomly or under the selection pressure generated by mitigation efforts."

Very interesting. My thesis for the new highly contagious variants is they are from the vaccinated because of the virus's escape mechanism. And on cue here we have a mention of the phenomenon in a medical study.

Oh well, postponing all judgement until it's peer reviewed. And while we're at it, how about study on head to head vaccinated vs unvaccinated mutation frequency.

> they are due to an escape mechanism sprung from the vaccinated

Hopefully you're aware that viruses accumulate mutations randomly by chance over time. The only way mutations can be outright stopped is through an immune response that completely neutralizes the SARS-CoV-2 virus. Determining if mutations originated in a vaccinated or unvaccinated host is a pretty useless endeavor that would only serve as fodder for divisive discussion. The fact is that mutations are expected to exist in high numbers due to neutral genetic variation alone.

With that said, worrying about viral evolution undermining the efficacy of the vaccine is a valid concern.

In general a leaky vaccine is one that keeps the host alive without necessarily stopping further infection and transmission. These conditions contribute to an environment that can allow the virus to accumulate mutations which eventually lead to immune escape [1][2].

Because the current mRNA vaccines are leaky and also induce an immune response highly targeted toward the spike protein RBD, there is concern that mass vaccination may create tremendous selective pressure which further enhances the fitness of the virus [3]. It's difficult to predict if such selective pressure will lead to enhanced virulence or infectiousness, but so far many variants of concern have mutations impacting the spike protein RBD. These mutations result in partial immune escape and manifest as increased infectiousness, reduced vaccine efficiency, and also reduced immunity in naturally infected individuals [4][5][6].

[1] The adaptive evolution of virulence: a review of theoretical predictions and empirical tests https://pubmed.ncbi.nlm.nih.gov/26302775/

[2] Why does drug resistance readily evolve but vaccine resistance does not? https://royalsocietypublishing.org/doi/pdf/10.1098/rspb.2016...

[3] Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein https://pubmed.ncbi.nlm.nih.gov/33909660/

[4] SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern https://science.sciencemag.org/content/early/2021/06/30/scie...

[5] mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants https://www.nature.com/articles/s41586-021-03324-6

[6] Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization https://www.nature.com/articles/s41586-021-03777-9

I think a good way to dumb this down is to use bacteria as an example. Most people know that improper use of antibiotics is leading to a surge of antibiotic-resistant superbugs. This is basically the same mechanism as far as I’m aware - evolution due to selection pressure.

If vaccinated people also keep wearing masks and social distancing, dangerous mutations should be much less likely.

> The fact is that mutations are expected to exist in high numbers due to neutral genetic variation alone.

Selection among these mutations will occur. The virus with the pre-vaccine, spike protein will be largely blocked from replicating, and mutations which have spike proteins that better enable infection will be selected for. Welcome to evolution ;)

One question I have is do viruses like covid ever reach peak fitness? I assume there are properties of the virus that at some point cannot be changed because they will negatively affect the ability of the virus to reproduce and with universal vaccination maybe it can be cornered in a local maximum where it can’t optimize reproduction further without losing some ability to reproduce first. This is how I keep the thought of eradication alive :)

One author is an MD, the other is an MBA (!!?!??!)

That doesn't smell right. It's also a pre-print without peer review yet.

As covid-19 has been shown to spread through animals, fingerpointing the blame for mutations at unvaccinated people is a farce and preventing them is an unachievable pipe dream.

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