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The major genetic risk factor for severe Covid-19 is inherited from Neandertals

biorxiv.org

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Re: The major genetic risk factor for severe Covid-19 is inherited from Neandertals

#21

Earlier quoted context omitted.

You don't need testing, just accurate body counts. You can see COVID hit Europe as a spike in excess deaths, even if you weren't testing. If there were currently a mortality spike in Bangladesh even higher than Europe's , it would not go unnoticed. Disappearing bodies is not that easy.

I mean.. China's official numbers are around 84k infected.. and much less dead than that. So...

The “count the bodies” technique is meant for situations where the country can’t test for COVID, either because it was too early or they don’t have the infrastructure. That technique won’t work on countries just willing to lie about it.

Re: The major genetic risk factor for severe Covid-19 is inherited from Neandertals

#22
post #8

Earlier quoted context omitted.

Given that there's a strong correlation between race and poverty in the US (via racism) and a strong correlation between poverty and infection rate which, it seems to mean poverty is a greater indicator than genetics. After all the genetic factor only comes into play after exposure, while poverty increases the likelyhood of exposure

is NYC with its highest rate of cases in the USA a generalization: density of people (which happens in poverty and in opulence, for different reasons) increases likelihood of exposure?

Population density really doesn't matter that much for a pandemic as infectious as COVID19. The number of people who live in the mountains or on a farm and only come into town every six months is very, very small.

The two big causes of massive early numbers of deaths, including in the northeast US (especially NYC, and NY state, NJ, and Philadelphia to a slightly lesser degree) and places like northern Italy, were

a) sending sick old people into old age homes. Other cities/states by and large did not do this. This drastically raised the average age of those who were infected in NYC, and caused the far higher death rates. 42% (!) of US deaths occurred in old age homes. Old age homes are pretty similar everywhere in terms of layout and design, regardless of local population density.

b) Assuming that ventilators should be used on every serious case, causing both damage from overoxygenation to healthy lung sacs and overdependence on mechanical respiration that doctors are having a tough time figuring out how to wean patients from. Those that warned three months ago (https://www.statnews.com/2020/04/08/doctors-say-ventilators-...) against ventilator overuse were completely vindicated in retrospect. This happened nationwide but most proportionately in NYC (in part because it was hit hard early so doctors were pioneers).

The big Western European countries hit hardest by the pandemic have 40-60 deaths per 10,000; the US is in the 30s, while states like Texas are in the single digits. NYC's death rate is 161 (!!); it singlehandedly prevented the US's death toll from being almost as low as Germany's. NYC's super-high death rate isn't replicated in the same way in other densely populated states that did not make the mistake of accidentally encouraging spreading of the disease among the elderly. Chicago, DC, and Boston were not hit anywhere as hard as NYC was.

Look, for example, at the NY Times dataset (https://www.nytimes.com/interactive/2020/us/coronavirus-us-c...). NYC's daily deaths peaked at about 10% of the cases, so we'll say 10% case fatality rate. Chicago's CFR is about 4%. Philadelphia's CFR is close to NYC, but Boston's is 6% and DC's is also about 4%. Basically, the NYC-Philly corridor handled this worse than anywhere else in the country.

Again, old age homes contributed 42% of COVID19 deaths, and largely due to big mistakes made in a portion of the northeast US. Those mistakes are no longer being made anywhere, nor is the "putting everyone on ventilators" mistake. This (plus the massive expansion in testing causing the average age of those testing positive to plummet) is why, although southern and western states' cases are rising (or in Los Angeles's case, never stopped rising from the start), deaths are not, and why national daily deaths continue to fall straight down from the mid-April peak.

Re: The major genetic risk factor for severe Covid-19 is inherited from Neandertals

#23
post #7

But how can this be, given that African-Americans, with far less Neanderthal ancestry than European-Americans, are dying of COVID-19 at a much higher rate in the US?

Maybe genetics aren't a very important part of mortality risk.

Re: The major genetic risk factor for severe Covid-19 is inherited from Neandertals

#24
post #6

If you have 23andme, the exact allele is not on the chip. However, a different allele is strongly associated with the region: https://you.23andme.com/tools/data/?query=rs10490770&filter_... The major A/A variant is listed as T/T on 23andme. If you have a result other than "T/T", you're likely to be in the high-risk group. refs: https://www.snpedia.com/index.php/Rs11385942 [not on 23andme] https://www.snpedia.com/inde…

Thanks for sharing these pointers!

A caveat for those who don't click through to the snpedia references: the "strongly associated region" only correlates well for Caucasians.

Re: The major genetic risk factor for severe Covid-19 is inherited from Neandertals

#26
post #6

If you have 23andme, the exact allele is not on the chip. However, a different allele is strongly associated with the region: https://you.23andme.com/tools/data/?query=rs10490770&filter_... The major A/A variant is listed as T/T on 23andme. If you have a result other than "T/T", you're likely to be in the high-risk group. refs: https://www.snpedia.com/index.php/Rs11385942 [not on 23andme] https://www.snpedia.com/inde…

This is actually the first time the 23andme results did anything useful for me. Thank!

How did you get it to pull on 23 and me. I have more Neanderthal variants than 99% of users so I’m super interested. Thank you for any help you can provide.

Re: The major genetic risk factor for severe Covid-19 is inherited from Neandertals

#27
post #6

If you have 23andme, the exact allele is not on the chip. However, a different allele is strongly associated with the region: https://you.23andme.com/tools/data/?query=rs10490770&filter_... The major A/A variant is listed as T/T on 23andme. If you have a result other than "T/T", you're likely to be in the high-risk group. refs: https://www.snpedia.com/index.php/Rs11385942 [not on 23andme] https://www.snpedia.com/inde…

That 23andme link doesn't work for me, it says no genes or markers found for rs10490770.

I couldn’t get it to work either, did anyone figure out how to view it on there?

Re: The major genetic risk factor for severe Covid-19 is inherited from Neandertals

#28
[Sars-Cov-2][Outcome risk] rs10490770 (Caucasisn only)

Risk: AG, GG (~15.5% of population?)

Safe: AA (~84.5% of population?)

--- SO, if 23andme says its T/T and its actually A/A(as herf said), than 84.5% of the population would have T/T via 23andme. I am confused then. If I have T/T through 23andme, am I at higher risk when ~85% of the population has the same thing?

Re: The major genetic risk factor for severe Covid-19 is inherited from Neandertals

#29
post #25

So in my 23andme it shows me as having the T/T genotype of this marker. Does that mean I do or do not have the at risk marker?

I think you're good. From what I've read, the high risk is C. T/T is modern human. C is neanderthal. So C/C - youre 3 times more likely to get sick. C/T youre 1.5times more likely to get sick.

Reference: https://www.gnxp.com/WordPress/2020/07/04/using-23andme-ance...

=== If this is wrong, someone correct me, but T/T results from 23andme seem to be 84.5% of the population (caucasion people), so YOU SHOULD BE FINE.

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