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So, they detected this variant half a year ago, and yet it didn't become prevalent. Delta rules the roost.

Is it possible that the heavy mutations detected on the A.30 variant also make it less contagious?




Even if A.30 was "more contagious", like Alpha, it isn't as contagious as Delta and thus would get outcompeted.

There's a lot of variants of concern. Its important to keep an eye on new variants, but don't worry about them until they cross the 1% or 5% mark. At that point, you can better theorize that they might be outcompeting the dominant strain.

You _really_ don't know that something is outcompeting until it reaches 50%. But by then its too late. The 1% or 5% points are still a month or two in advance of the 50% crossing, in both Alpha and Delta.

So that's where I keep my attention: at the 1% and 5% points. A variant gotta get to 1% before it can reach 50% of the world ya know?


At the very least, it seems that you cannot be reinfected by A.30 if you had Delta recently, otherwise they would be both spreading at the same time.


You probably can, it just means that the R in this scenario is very small. If R is below 1 it will fade away.


How does viral outcompetion work? How would Delta prevent A.30 from thriving? Why won't we become infected by Delta and A.30?


> How does viral outcompetion work?

Basically one spreads faster than the other so after a few iterations almost all of new cases are the new variant.

> How would Delta prevent A.30 from thriving?

Directly by driving up immunity, indirectly by coercing people to take steps to slow the spread of delta, which also slows the spread of a.30. Things like vaccination, social distancing, mask wearing etc...

> Why won't we become infected by Delta and A.30?

Because Delta probably give you significantly more immunity than a vaccine. Specifically infection gives both more robust and stronger immunity than the vaccines.


> Specifically infection gives both more robust and stronger immunity than the vaccines.

Isn't there evidence that says the opposite? And that immunity due to infection is much more variable between individuals and infections, due to how the immune system responds to the virus.


https://www.medrxiv.org/content/10.1101/2021.08.24.21262415v...

> SARS-CoV-2 naïve vaccinees had a 5.96-fold (95% CI, 4.85 to 7.33) increased risk for breakthrough infection and a 7.13-fold (95% CI, 5.51 to 9.21) increased risk for symptomatic disease. SARS-CoV-2-naïve vaccinees were also at a greater risk for COVID-19-related-hospitalizations compared to those that were previously infected.

> Conclusions This study demonstrated that natural immunity confers longer lasting and stronger protection against infection, symptomatic disease and hospitalization caused by the Delta variant of SARS-CoV-2, compared to the BNT162b2 two-dose vaccine-induced immunity. Individuals who were both previously infected with SARS-CoV-2 and given a single dose of the vaccine gained additional protection against the Delta variant.

Also just in terms of baseline beliefs based on the physical world, I would assume that the vast majority of the time an infection would be more protective than a vaccine.


>Also just in terms of baseline beliefs based on the physical world, I would assume that the vast majority of the time an infection would be more protective than a vaccine.

It is also orders of magnitude more deadly. Vaccines are proven to be much safer than getting Covid.

This is one preprint study comparing natural immunity to the Pfizer vaccine. It is interesting and may hold up after peer review. However, we have to be careful drawing broad conclusions and over interpreting these results.

The danger is that we are already seeing many groups pointing to this study and trying to read this as meaning we should not be getting vaccinated, because obviously getting covid is better. We should not forget that in 2020 and into 2021, despite significant lock downs and enforced/encouraged masking, and without widely and globally available vaccinations we lost about 5 million people to Covid. Skipping vaccines in favor of "natural" immunity is a path to continued carnage.


People are not usually saying getting covid is better (not without many qualifiers anyway), they are saying that if you already had covid, getting shots might have bad risk/benefit ratio. (you get all the risk for small additional protection).


It might have a bad risk/benefit ratio. The preliminary evidence I've seen suggests a good risk/benefit ratio.

https://www.nature.com/articles/d41586-021-02795-x

>Those who had recovered from COVID-19 months before receiving their jabs harboured antibodies capable of defanging the mutant spike, which displays much more resistance to immune attack than any known naturally occurring variant. These peoples’ antibodies even blocked other types of coronaviruses. “It’s very likely they will be effective against any future variant that SARS-CoV-2 throws against them,” says Hatziioannou.


>People are not usually saying getting covid is better (not without many qualifiers anyway), they are saying that if you already had covid, getting shots might have bad risk/benefit ratio. (you get all the risk for small additional protection).

You should really check what people are saying on random posts on Facebook.


I haven't seen any evidence for that, but I've sure seen it claimed a lot.


I've seen it repeated pretty extensively on r/covid19, which I have to say comes across as a much more scientifically robust site for covid information than Hacker News. The quality of information here isn't much above Facebook.


>I've seen it repeated pretty extensively on r/covid19, which I have to say comes across as a much more scientifically robust site for covid information than Hacker News. The quality of information here isn't much above Facebook.

I 100% agree with you on the quality of information here vs. there. It is much, much more strictly moderated. But with that moderation, that subreddit does not recommend going out and getting COVID in lieu of a vaccine. Even if initial response is better for COVID.

COVID + Vaccine is by far the best, but that doesn't mean you should skip the vaccine to make sure you go the 'rona frst.

Vaccine + Vaccine (and maybe + vaccine) is, by far, the safest combination for pretty much everyone people.


The same way that Delta has decimated Flu Type B/Yamagata to the point that some are whispering that Flu Type B/Yamagata has gone extinct. (The Flu is still around, but Type B/Yamagata was very, very common before COVID19 hit. It hasn't been seen for almost 1.5 years now)

Its not like "Delta-variant" gives you immunity to Flu Type B/Yamagata. But people around the world are masking up and locking down (well, in 2020 anyway). People's behaviors change when a large-scale pandemic like this occurs, and the weaker viruses die out.

Even ignoring that, COVID19 forces an immune response. Yes, this immune response includes memory-cells (which remember COVID19's signature), but it _ALSO_ increases other immune cells (Neutrophil, killer-T cells, among others) which will hunt down any virus more effectively. This effect is temporary, but still a big enough effect to see the body fight off other diseases a bit better after getting sick from anything.

So even though COVID19 / Delta doesn't give you any immunity (ie: memory cells / antibodies) to Flu B/Yamagata, you see Delta outcompeting it and driving Flu B/Yamagata to extinction.

--------

Delta transfers memory-cell responses + antibody responses (two attributes of "memory immunity") against COVID19, and Alpha, and other variants. Sure the disease is evolving, but its not like these antibodies are totally useless against the virus within the same line.

COVID19 simply doesn't evolve as quickly as the flu does.

--------

This effect, in reverse, was seen in 2020 where recipients of the standard Flu shot had something like a 5% lower chance of getting COVID19. The temporary "immune response" that your body built up for the Flu vaccine had a minor (but measurable) effect on COVID19.

Getting sick with _ANYTHING_ makes it harder for other viruses to attack you. Your body just goes into overdrive making various white blood cells.


You asked a good question that I’ve wondered as well. Basically someone has to show that immunity to one variant confers immunity to another, which is not at all obvious since presumably they have different epitopes. I guess what people are suggesting is that the epitopes are distinct enough that a targeted vaccine might not cover both, but not so distinct that they behave like separate infections in vivo. But I would hope that an expert can chime in and shed some light here.


>I guess what people are suggesting is that the epitopes are distinct enough that a targeted vaccine might not cover both, but not so distinct that they behave like separate infections in vivo. But I would hope that an expert can chime in and shed some light here.

There are sooooo many papers that prove this -- stop pretending you are too important/lazy/etc to search for them yourself because you want to write some anti-vax BS.


The hell? I’m not anti-vax, some of my PhD work was in virology. I just don’t care to keep up with the literature. Take your beef somewhere else.


Same question, especially that if someone is infected with delta he can only infect someone with delta. So delta can be outperformed at the person level only if the person is infected by both variant at the same time.

For me the only way a variant can be outperformed is that all people who get infected get also infected with the other variant OR the first variant for whatever reason stop being transmissible


>For me the only way a variant can be outperformed is that all people who get infected get also infected with the other variant OR the first variant for whatever reason stop being transmissible

What you are saying isn't logically sound.


Because being infected by the successful, fast-spreading one confers you a measure of immunity against the less successful variant, thereby directly suppressing it.


> Is it possible that the heavy mutations detected on the A.30 variant also make it less contagious?

That wouldn't surprise me. The spike is central to how SARS-CoV-2 is so infectious. If the virus mutates the spike too much, it might evade the vaccines, but at the cost of being less infectious.

What's surprising is this research says, in vitro, A.30 is more infectious.

Regardless, as you and others say, in real world conditions A.30 doesn't appear to out compete Delta.


>Is it possible that the heavy mutations detected on the A.30 variant also make it less contagious?

100%. This strain hasn't been seen since May. It has already died out because of Delta.

All of these discussions are academic -- we really are only talking about if a Delta variant can gain these mutations and really wreck havoc. And the answer is "probably not" (for a while, anyways)


the results in the paper suggest, the mutations facilitate viral mechanisms of entry and antibody evasion.

efficacy of Oxford, Pfizer, and hetero-innoculation with both were examined, indications were given of reduced efficacy of either vaccine alone vs CoV A.30. The combination of both vaccines[hetero-inocculation] was associated with higher efficacy vs A.30

the mutations appear in vitro; to confer inhibition of vaccine induced antibody binding; enhanced cellular entry; enhanced pulmonary[lung] trophicity[targeting]

relative efficacies of moderna; Johnson&johnson; vs Oxford; Pfizer were not examined.


genuinely asking, how do we actually know the delta variant is real, and is the dominant variant causing the current cases? do people actually get tested for specific variants, or is it just a generic covid test?


It depends where you live. The UK was an early[0] leader in sequencing a lot of their cases. They hit 600,000 sequenced cases in July[1].

That said, if you just want to know what proportion of the population has delta, you don't need to sequence that many cases. The point of sequencing a large fraction of cases is to catch emerging variants, that wouldn't be likely to be caught otherwise. But to know whether Delta is 30%, 50%, or 70% of cases, you just need a good random sample, not a particularly large one, and I imagine you can do that at the labs where the PCR tests are being run.

(at one point, I recall that the UK had a test that matched on three distinct sites on the virus, and they found that one of those sites would turn up negative for a particular variant, so they were able to use that as a proxy for the spread of the variant. I don't remember if that was Alpha or Delta though, and obviously it's no replacement for sequencing)

[0] https://cen.acs.org/analytical-chemistry/sequencing/200000-c...

[1] https://www.gov.uk/government/news/uk-exceeds-600000-covid-1...


UK publishes detailed reports on variant surveillance via genetic sequencing, https://www.gov.uk/government/publications/investigation-of-...

US does statistical sampling and also prevents patients from being told about variants, https://news.ycombinator.com/item?id=28419280


Not every test will tell you which variant it is, but they do some extra testing here and there to track which variants are spreading.


NZ had until recently sequenced 100% of its cases, and used that sequencing information to map person to person infection linkages. This included all of the people in the mandatory 2-week quarantine at the border. So in NZ, yes, every case was tested for specific variants. Delta does seem to be real.


Genomic surveillance; separate from the routine COVID tests, performed on a statistically significant sampling of them.

https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-s...

https://www.cdc.gov/coronavirus/2019-ncov/variants/cdc-role-...


Some small subset of COVID tests are sent to larger labs to perform a more detailed genetic test to determine specific variants. The prevalence of different variants within that set is extrapolated to the population of the region from which it originated.

If the lab finds that 87% of the samples from Adam's College are of the Omega Mu strain, then it's assumed 87% of total cases at Adam's College to be Omega Mu variant.


In Washington state, a percent of positive tests are sent to the dept of health for variant sequencing. You can see the published results by week. Delta has outcompeted every other variant for several months. All covid is essentially delta.

See page [pdf] 5 on this: https://www.doh.wa.gov/Portals/1/Documents/1600/coronavirus/...

It is updated every Wednesday


Not all cases are tested for which variant, but those that are are catalogued.

I've been watching the delta variant take over the world over the past several months here: https://covariants.org

(dark green is delta)


There are multi tests today which can differentiate between variants without sequencing.

There is also a way to differentiate on some RT-PCR tests (but not all), depending on how they are made.


They sample the swabs and do full sequencing for those selected.


Also see nextstrain.org for interesting data.




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