The major genetic risk factor for severe Covid-19 is inherited from Neandertals
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Re: The major genetic risk factor for severe Covid-19 is inherited from Neandertals
#2Standard disclaimer that this is a preprint that has not been peer reviewed.
Re: The major genetic risk factor for severe Covid-19 is inherited from Neandertals
#3Svante Pääbo , one of the preprint authors, is the head of the Max Planck Institute for Evolutionary Anthropology.
https://en.wikipedia.org/wiki/Svante_P%C3%A4%C3%A4bo . He is known for his work in assembling the Neanderthal and Denisovan genomes.
Of particular note in this paper, the genetic variants in the genomic locus discussed are found in 30% of South Asian populations: India and Bangladesh. The highest frequency occurs in Bangladesh, where more than half the population (63%) carries at least one copy of the Neandertal risk variant and 13% is homozygous for the variant. The risk variant is 8% frequency in Europe.
The hg19 location of Genetic variants in LD (r2>0.99) with rs11385942 in Eurasian populations can be viewed here at the UCSC genome browser: https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=ch...
The genome wide association study that points out this area of the genome is here : https://www.nejm.org/doi/full/10.1056/NEJMoa2020283 . At this "locus 3p21.31, the association signal spanned the genes SLC6A20, LZTFL1, CCR9, FYCO1, CXCR6 and XCR1."
Three of the genes, XCR1 CXCR6 CCR9, are involved with chemokine receptor activity and G-protein coupled chemoattractant receptor activity.
Re: The major genetic risk factor for severe Covid-19 is inherited from Neandertals
#4Svante Pääbo , one of the preprint authors, is the head of the Max Planck Institute for Evolutionary Anthropology. https://en.wikipedia.org/wiki/Svante_P%C3%A4%C3%A4bo . He is known for his work in assembling the Neanderthal and Denisovan genomes. Of particular note in this paper, the genetic variants in the genomic locus discussed are found in 30% of South Asian populations: India and Bangladesh. The highest frequen…
Also only ~4% in the US, and virtually absent in Africa.
Re: The major genetic risk factor for severe Covid-19 is inherited from Neandertals
#5"Here, we show that the risk is conferred by a genomic segment of ~50 kb that is inherited from Neandertals and occurs at a frequency of ~30% in south Asia and ~8% in Europe."
Hmmm...thus far, the mortality per capita from Covid-19 has been much higher in Europe, especially western Europe, than in south Asia. Not saying that couldn't change, but the weekly mortality peaks in western Europe were literally an order of magnitude higher than for Bangladesh, India, or Pakistan. So either this finding is flawed in some way, or (perhaps more likely) even the biggest genetic risk factor for severe Covid-19 is not that big of a factor, and what's going on is mostly not genetic.
Re: The major genetic risk factor for severe Covid-19 is inherited from Neandertals
#6If 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/index.php/Rs10490770
Re: The major genetic risk factor for severe Covid-19 is inherited from Neandertals
#7But 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?
Re: The major genetic risk factor for severe Covid-19 is inherited from Neandertals
#8But 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?
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
Re: The major genetic risk factor for severe Covid-19 is inherited from Neandertals
#9"Here, we show that the risk is conferred by a genomic segment of ~50 kb that is inherited from Neandertals and occurs at a frequency of ~30% in south Asia and ~8% in Europe." Hmmm...thus far, the mortality per capita from Covid-19 has been much higher in Europe, especially western Europe, than in south Asia. Not saying that couldn't change, but the weekly mortality peaks in western Europe were literally an order of…
Or maybe the stats used for the data in European countries are flawed...or there is less testing in the latter countries....
Re: The major genetic risk factor for severe Covid-19 is inherited from Neandertals
#10But 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?
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
Other factors may be obesity ( https://www.minorityhealth.hhs.gov/omh/browse.aspx?lvl=4&lvl... ) , diabetes ( https://www.minorityhealth.hhs.gov/omh/browse.aspx?lvl=4&lvl...) and Vitamin D deficiency ( http://www.cooperinstitute.org/2019/09/24/african-americans-... ).