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Comment by mattrighetti | Hacker News Reader

The fact that this has been discovered in Africa doesn’t mean that it originated there in the first place.

> Several scientists said they suspected that the variant had been spreading undetected in countries with lackluster sequencing efforts before it surfaced in Botswana and South Africa, giving it more time to scatter globally. Nevertheless, European nations did not find the variant until after South Africa alerted them to it, demonstrating the gaps in their own surveillance efforts. [0]

More on this can also be found here [1].

[0] https://www.nytimes.com/2021/11/27/world/africa/coronavirus-...

[1] https://www.linkedin.com/posts/graemecodrington_interesting-...

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Given the large amount of mutation in this variant, theory point to high likelihood of this being evolved from a single individual with compromised immune system, likely a person in advanced stages of HIV infection.

Source: https://yourlocalepidemiologist.substack.com/p/new-concernin...

Globally speaking, most of the HIV positives live in sub-saharan Africa, with South Africa having 17.30% of adults carrying HIV, and countries around it in similar ballpark. This points to the variant being evolved in South Africa or its neighbors

Source: https://en.wikipedia.org/wiki/List_of_countries_by_HIV/AIDS_...

This is correct, but I don't believe it devalues the original comment any less. Any part of the world where vaccination rates are lower allows (I assume) any variant to grow in that region, and then makes it easier to export to other parts of the world.

Given the apparently low efficacy of the current batch of vaccines in preventing infection and transmission, I'm not sure that it's any harder for variants to occur in, say, New Mexico than South Africa. If the case rates are higher, the odds of variants is higher.

I'm not sure this is true. Mutation happens with approximately fixed probability with each copy made.

"peak viral load did not differ by vaccination status or variant type"[1]

[1]: https://www.thelancet.com/journals/laninf/article/PIIS1473-3...

I read somewhere that the new strains are probably created inside people whose immune system is not able to clear the virus, thus allowing it to mutate and create new strains.

I guess those people would be more likely to be exposed at all in countries with less vaccination though.

That seems to be disputed too, this is an interesting read: Increases in COVID-19 are unrelated to levels of vaccination across 68 countries and 2947 counties in the United States.[0]

> At the country-level, there appears to be no discernable relationship between percentage of population fully vaccinated and new COVID-19 cases in the last 7 days

> Notably, Israel with over 60% of their population fully vaccinated had the highest COVID-19 cases per 1 million people in the last 7 days. The lack of a meaningful association between percentage population fully vaccinated and new COVID-19 cases is further exemplified, for instance, by comparison of Iceland and Portugal. Both countries have over 75% of their population fully vaccinated and have more COVID-19 cases per 1 million people than countries such as Vietnam and South Africa that have around 10% of their population fully vaccinated.

> There also appears to be no significant signaling of COVID-19 cases decreasing with higher percentages of population fully vaccinated

Of course that could be different for third world countries.

[0] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8481107/

That article is garbage, full of randomly picked data points, not accounting for other variables, blatant misinterpretations and convenient omissions. Anti-vaxxers love posting it.

Can you elaborate more on that? Legitimate question, I came across this a couple days ago on some other thread here on HN.

Can you think of some issues with this study? legitimate question.

Looking at one data point here. Israel. The data point pretty much represents the peak of the wave caused by the Delta variant. The story in Israel goes that the vaccines worked so well against the previous variants that the entire country went back to normal. But with 60% of the population vaccinated and Delta the effective R number is easily over 1 when there's no other measures in place. Once Israel introduced some new measures (and booster shots), most of the measures are around limits to not-vaccinated people btw, their case rate went down by a factor of 20!

So what does this tell us about vaccines, covid, and this "study"?

I can think of many actually, but this is not my field of expertise so I don't want to jump on erroneous conclusions and I want to pay close attention to what I say, other than get feedback from others that for sure know a lot more than me. Just to get things straight, I am in no way saying that vaccines are not effective, there is strong evidence that indicates the contrary.

I was responding to a user who claimed that the more covid goes around, the more it mutates, and as far as I understand it's what viruses do and therefore is a correct statement.

I then linked this study and cautiously pointed out that it is "disputed", which may still be the wrong term in that case or I was erroneously giving too much credit to the paper itself.

You then point out that the study highlights the Delta variant peak when dealing with the Israel data, and I could agree on that.

What the study is trying to highlight, as far as I can tell, is not to undervalue *vaccination which has strong evidence ww to greatly lower hospitalisation and death risk from covid infection*, but it instead tries to tell that even in vastly vaccinated communities there are a lot of cases and they can't be distinguished from those in communities with lower vaccination rate.

So my argument was: if cases are rising in largely vaccinated communities, the virus will inevitably mutate in those communities too and it is not a pattern only related to third world countries with low vaccination rates.

I don't think the study shows that either. Generally the bulk of the cases and especially hospitalizations and deaths have been amongst unvaccinated. When you have 40% of a country unvaccinated and when those 40% tend to form social groups and closer connections you can't really look at the country as a whole.

At any rate, the methodology of the paper is just way off. If you truly wanted to understand the correlation between vaccination and infection rates you need to try to control for other factors. That is just experiment design 101. If you control for nothing while there are other significant factors then you get nothing. If the paper is saying "there can be high covid rates with 60%-70% vaccine coverage and the delta variants" then sure, but also duh.

"Experts: Vaccine Immunity Waning, Signs Israel Facing Fifth COVID Wave"

https://www.haaretz.com/israel-news/experts-vaccine-immunity...

Right (also "in part because the vaccination of children takes time to come into effect").

They are hovering around R=1 with very minimal restrictions and still a significant amount of people that won't take the vaccine ("citing the fact that a third of the population remains unprotected. This refers to 670,000 unvaccinated Israelis, more than a million people who haven’t received the booster, and children under 12"). They're making up for the vaccine coverage to some extent by:

1. Lots of people got sick. Israel has a young population and a very strong healthcare system so they were able to manage a very high daily case rate per capita.

2. Booster shots.

3. And now, vaccinating children.

I don't think anyone knows yet exactly what sort of waning effect you have after the third booster. It's also hard to say what portion of the change is behavioral changes vs. the vaccine's wane.

Now the new variant completely changes the calculus yet again.

Lots of criticism collated at the article's PubPeer page:

https://pubpeer.com/publications/693A0D3B374ACED0103ADDEA0D9...

The PubPeer browser extension is worthwhile: https://pubpeer.com/static/extensions

And that's how this stuff keeps spreading. People who don't really understand what they are passing on passing it on as though it means something to them. If you didn't really understand it, why did you pass it on?

The authors haven’t done any questionable transforms of the dataset - its literally the whitehouse dataset as a scatterplot. How is it garbage ?

You can’t compare developing countries that barely test anyone with Portugal which has strong and robust testing. Likely that tons of infections get untested so to prove that vaccine don’t work just because some other country with lower vaccination has less cases makes absolutely no sense. Any epidemiologist knows that and this is why this garbage analysis.

What you do is that you compare within the same country where conditions are similar. It’s the same everywhere, virus spread more and leads to more deaths and hospital cases among the unvaccinated.

It doesn't prove it originated there but all of the evidence points that it doing so.

Also [1] doesn't mention what countries the diplomats were coming from my guess would be an African country.

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