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Covid 19 and the Neanderthals

27 December 2020

No, this is not a jokesey headline. At https://phys.org/news/2020-12-covid-neandertals.html … but to read the full story go to www.nature.com/articles/s41586-020-2818-3 … could Covid 19 have wiped out the Neanderthals? At least it recognises that their disappearance is not just due to superior modern humans and could have something to do with natural disaster. This is of course expanding the covid hype into the remoter past – but see https://doi.org/10.1101/2020.12.11.422139

This is in fact a genetic study and the Neanderthal link is defined from the genomes of two skeletal remains. It pushes into the mystery surrounding their disappearance by raising the possibility of an epidemiic – around 40,000 years ago. The headline is designed to capture attention. The full article might bore you stiff – but it is full of fascinating ideas. It also poses the question – did modern humans really out compete the Neanderthals? It asks – could mitochondrial Eve, her contemporary Y chromosome Adam, or even the Out of Africa hypothesis, be simply convenient fiction. Wow. What a piece of good thinking at Phys.Org.

They then ask – what does the coronavirus have to say about the issue. Svante Paabo, the geneticist, has made a good living out of finding genes inherited from Neanderthals. In 1997 he led the team that sequenced mtDNA from Neanderthal skeletal material. In september of this year, 2020, Paabo and team announced that the covid 19 risk factor is directly inherited from Neanderthal genes. Severe covid 19 is associated with genetic variants in 6 genes within a 50K base pair long region of chromosome 3 that is derived directly from a Neanderthal heritage. Similar investigations have also identified a protective Neanderthal haplotype on chromosome 12 that reduces the risk of severe covid 19 and a protective region on chromosome 9 that is associated with A, B and O blood groups. So, that is where that idea came from.

They report at bioRxiv, the Biology preprint portal, that another Neanderthal variant is pulling the strings of covid susceptibility. DPP4 is involved in immune function and glucose metabolism. It is also the receptor of the MERS coronavirus. Although other researchers claim DPP4 is not a SARS  Cov-2 receptor, these are now considered findings hard to ignore. Inhibitors used to treat diabetes appear to have effects on Covid 19 patients etc. Don't get covid 19 if you have diabetes problems. 

The DPP4 gene is not too far away from a long defunct remnant centromere found nearby in the ch2q21.3-q22.1 region [whatever that is]. There is also an additional vestigial telomere sitting down in the q13 band. What are these  structures doing here? Here is the rub. If pressed for a one line answer to the question of what is it that makes us human, an excellent answer might be the fusion of two small ape chromosomes to make the human chr2. Do Neanderthals have a fused chr2?

Of course they do. In fact, they seem to have the same version of the speech gene, FOXP2 which Paabo put on the map in 2002. Human FOXP2 differs from the chimpanzee version in two key places. It was famously mutated in the KE family from Britain who all had a specific disability in their use of consonants. In the more recent covid risk studies Paabo searched for single nucleotide polymorphisms using data from the 1000 Genomes Project, then checked them with the Covid 19 Host Genetics Initiative to see if Neanderthal haplotypes for DDP4 were associated with disease severity.

Now, we have the PhysOrg chap kicking in – the problem with this line of work is that we don't have that much sequence data to tell us what makes a Neanderthal a Neanderthal. Good thinking once again. There are just a few genomes available from skeletal remains – at 120,000 and 50,000 years ago. These came from Europe and southern Siberia. They are statistical shortfalls. One point, they claim, regarding the current covid outbreak and the research frenetically going on behind the scenes, is that blind medicine is no longer enough to satiate the interested parties. The Phys Org author admits he has taken some under the belly shots at paleo genetics, well deserved in my opinion, but says there was a good reason for doing so. There is no such thing as a reference sequence – it is completely arbitrary. What an admission. Updates and improvements are made to various reference sequences from time to time but no true reference sequence will ever be had.

In contrast to the MERS DPP4 receptor, no receptor variants have emerged as a risk locus for severe covid 19. However, many of the other genes associated with SARS cov-2 infection process and life sycle have come to light. For example, four variants robustly affect lung tissue. These variants are more common in European than in Asian populations.

Then we get to the nitty gritty as vaccines are rolling out. The question is, whom might the vaccines help – and who not. Some researchers have found that some anti spike monoctonal antibodies from covid 19 patients have increased infectivity. This might be pertinent to those vaccines that involve RNA. 

This ranks as one of the best Phys Org posts in recent times. My congratulations to the author. I have only one caveat. The outbreak and subsequent evolving of covid 19 around the world does appear to suggest, weakly rather than strongly, there is an atmospheric dimension. After all, what is bird Flu but an atmospheric phenomenon. While this might be able to map out how covid 19 may evolve in the next year or so, and why some regions were more infected than others, the whole question of disease from space is ignored. Why? It would account for similarities at the point of Neanderthal extinction as well as the persistence of the common cold. One suspects that genetic research will eventually come to the same gateway. See for example George Howard's web site https://cosmic tusk.com without advocating a full on acceptance of the theory. It is something to bear in mind while absorbing what the likes of Paabo are saying.

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