Neanderthal gene protective of COVID19

[Titane]

OK! page 7?

 

In populations outside of Sub-Saharan Africa, the protective
alleles at both rs4767027-T (the OAS1 pQTL) and rs10774671-G
(the OAS1 sQTL) are found on a Neanderthal haplotype34, which
was passed on to modern humans ~50,000–60,000 years ago35.
The correspondence between the previously described gene flow35
from Neandertals at this locus and the haplotype associated with
protection against COVID-19 in the GWAS22 was recently demonstrated34. Even though these two single-nucleotide polymorphisms
(SNPs) share a haplotype, their evolutionary histories differ. The
rs4767027-T allele is derived from the Neanderthal lineage, whereas,
for the rs10774671-G allele, Neanderthals preserved the ancestral
state. OAS1 alternative splicing regulated by the rs10774671-G allele
increases the isoform p46, which has a higher enzymatic activity
against viruses than the p42 isoform36 and is the only OAS1 isoform
robustly upregulated during infection26. Although further studies
are needed to fully elucidate the functional relevance of the pQTL
and sQTL for OAS1, the antiviral activity of the gene products is
higher for the Neandertal haplotype than the common haplotype
in Europeans28. In Europeans, the Neandertal haplotype has undergone positive selection26, and the rs4767027-T allele reaches an
allele frequency of 0.32. Using MR and measurements of circulating proteins, we demonstrated here that increased OAS1 levels of
the Neandertal haplotype in modern-day individuals of European
ancestry confer this protective effect.

I think 23andMe identified this area as Neanderthal.
If you don't have the result for this snp, maybe you have the Neanderthal segment where this SNP is located ...

This is my chromosome 12 and that of my father.
The red line represents where rs10774671 should be located. genomic position: 113,357,193
(if I didn't make a mistake):

Attachment 43643

I am GG, but I only have one segment identified Neanderthal by 23andMe

Here is my chromosome 12. I highlighted the same area - mine would show as homozygous but I am AG.

B4BA5DBC-D988-4331-9C10-99D505C65FB8.jpeg

I guess we will have to ask...

[FionnSneachta]

That is probably quite rare. I'm sure that you're fine.

But I'm one in a million!

I am joking and agree that it has very likely provided me with sufficient immunity.

[Arnfried]

To bad, I got the A/A ones.
With 303 Neandertal's variants I didn't get this one which could allow me to throw up these awful masks!

[J Man]

But I'm one in a million!

I am joking and agree that it has very likely provided me with sufficient immunity.

And don't forget the luck of the Irish!

[Titane]

To bad, I got the A/A ones.
With 303 Neandertal's variants I didn't get this one which could allow me to throw up these awful masks!

It does not change our daily lives. Even the people who have received the vaccine still have to wear masks. And they protect us from all these other viruses that we don’t have this year...

[1938helerich]

I don’t see this on the raw data on 23andme. Must be on the older ones.

[Webb]

I am 100% European, on paper and per my dna and I am rs10774671(A;A). Bummer.

[Titane]

I don’t see this on the raw data on 23andme. Must be on the older ones.

Yes apparently... I have it also on Ancestry but again an older version (2016). I wonder if it's the case for their new version as well.

[coffeeprince]

Yes, it's not found on the 23andme v5 chip, but it's available on both FTDNA and AncestryDNA chips that I can see.

[ThirdTerm]

Another study by Zeberg and Pääbo (2021) is more comprehensive in scope, looking into global frequencies of this Neandertal haplotype protective against COVID-19 on chromosome 12, which contains parts or all of the three genes OAS1, OAS2, and OAS3.


Fig. 3.

Geographic distribution of the allele indicative of the Neandertal haplotype protective against severe COVID-19.

COVID-19 Protection and Geographic Distribution.
We find that the index variant of the protective haplotype in the GenOMICC study (rs10735079, P = 1.7e-8) matches all three Neandertal genomes available. The relative risk of needing intensive care is reduced by ∼22% per copy of the Neandertal haplotype (under the rare disease assumption, odds ratio [OR] = 0.78, 95% CI 0.71 to 0.85). As expected given the phylogeny (Fig. 2), almost all of the alleles cosegregating with the protective allele of the index SNP are found in the Neandertal genomes (34 of 35 called SNPs; see SI Appendix, Table S2, which, in contrast to Fig. 1, includes data contributed by 23andMe to HGI).

Today, the haplotype is almost completely absent in African populations south of the Sahara but exists at frequencies of ∼25 to 30% in most populations in Eurasia (Fig. 3). In the Americas, it occurs in lower frequencies in some populations of African ancestry, presumably due to gene flow from populations of European or Native American ancestry (33).

In addition to the splice acceptor site, the Neandertal haplotype contains a missense variant (rs2660) in OAS1, a missense variant (rs1859330) and two synonymous variants (rs1859329 and rs2285932) in OAS3, and a missense variant in OAS2 (rs1293767). Three of these Neandertal-like variants are ancestral and occur in Africa (rs2660, rs1859330, and rs1859329), whereas two are derived in Neandertals (rs2285932 and rs1293767).

https://www.pnas.org/content/118/9/e2026309118