A genetic link to a virus susceptibility?
Oy.
Just what we needed.
If the facts about COVID-19 weren’t bad enough, we now discover some of the risk factors may be in our genes.
Yes, indeedy, if you’ve taken a DNA test for genealogy, you too may be able to find out if you need to do more hiding-under-the-bed.
Which is where The Legal Genealogist is… and may remain…
Because — sigh — an extra dose of susceptibility to COVID-19 may well be in my genes.
This issue popped up in my Facebook feed yesterday as a post from fellow genealogist Lori Thornton. There was a newly-published scientific study identifying the Neanderthal origin of specific genetic markers linked to a higher susceptibility to respiratory failure among COVID-19 patients.
It’s a preliminary study that hasn’t been peer-reviewed — meaning it’s based on data that other scientists haven’t had a chance yet to look at and either confirm or refute.
The authors are Hugo Zeberg and Svante Pääbo. Zeberg is with the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany; Pääbo is with the Karolinska Institutet at Stockholm, Sweden. Their study, “The major genetic risk factor for severe COVID-19 is inherited from Neandertals,”1 is available online at bioRxiv, which explains that it is:
a free online archive and distribution service for unpublished preprints in the life sciences. It is operated by Cold Spring Harbor Laboratory, a not-for-profit research and educational institution. By posting preprints on bioRxiv, authors are able to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals.2
So this is not take-it-to-the-bank science. This is we-think-this-could-be-an-issue science. But here’s the kicker: this study just says the suspect genetic marker is of Neanderthal origin. There’s another study that it relies on — and it is a peer-reviewed study — that documents two specific risk factors for worse outcomes for COVID-19 patients: blood type A and “a … gene cluster as a genetic susceptibility locus in patients with Covid-19 with respiratory failure.”3 The documented risk, at this time, is only for Caucasians.
Sigh…
Guess what this Caucasian’s blood type is?
And guess what my genetic susceptibility locus shows?
Yup. I’m blood type A, and I do show that genetic susceptibility, although — I’m glad to say — at a reduced level.
And here’s how I know.
The raw data from the various genealogical DNA testing companies can be downloaded as files we can then review to see what values are shown at various locations. In my case, I looked at my raw data files from 23andMe, Ancestry, and Family Tree DNA. And they all say the same thing: at the specific genomic marker, rs10490770, I have the mixed marker C/T.
If I’d had T/T (one T marker from each parent), I’d have been at lowest risk. If I’d had C/C (one C marker from each parent), I’d be at highest risk. With the mixed marker C/T (one C from one parent and one T from the other), it’s a mixed bag: some additional risk. And in any case, nobody’s entirely sure how much risk. At SNPedia, it’s been assigned a magnitude of 1.7 for the mixed markers (somewhere just below the “looks interesting enough to be worth reading” stage) and 3 for the high risk markers (“Probably worth your time”).4
I’d love to know which parent to blame, but there aren’t any clear indicators. My paternal half-brother doesn’t have any C marker, but then neither do any of my mother’s siblings who’ve tested.
Sigh…
I think I’ll go back to binge-watching Hamilton… it’s a sure bet I’m not going out and about any time soon…
Cite/link to this post: Judy G. Russell, “Maybe in our genes???,” The Legal Genealogist (https://www.legalgenealogist.com/blog : posted 5 July 2020).
SOURCES
- Hugo Zeberg and Svante Pääbo, “The major genetic risk factor for severe COVID-19 is inherited from Neandertals,” bioRxiv, Cold Spring Harbor Laboratory (https://www.biorxiv.org/ : accessed 5 July 2020). ↩
- “About bioRxiv,” bioRxiv, Cold Spring Harbor Laboratory (https://www.biorxiv.org/ : accessed 5 July 2020). ↩
- David Ellinghaus, Ph.D., et al., “Genomewide Association Study of Severe Covid-19 with Respiratory Failure,” New England Journal of Medicine, posted 17 June 2020 (https://www.nejm.org/ : accessed 5 July 2020). ↩
- See “rs10490770,” and “Magnitude,” SNPedia (https://snpedia.com/ : accessed 5 July 2020). And note that the SNPedia explanation includes the fact that it shows these as A/A, A/G and G/G while the testing companies use the T/T, C/T and C/C designations. So if you’re looking at your raw data, look for TT (good), CT (not so good) or CC (possibly bad). ↩
You state that each of the several labs provided raw data showing your result for rs10490770. I similarly have tested at those three but only FTDNA has a result for that location (in my case a TT, the “lowest risk”). Neither Ancestry nor 23andMe provided any result for that location, begging the question, “why do you have something there and I do not?” Is this a “which chip was used for your/my test?” issue?
Yes. Some of the newer tests will not show a result at this location.
Wallace, My 23&Me data does have a result at rs10490770 but I tested there some years ago…
This is a factor of what chip you tested on, just as Wallace suggests.
Exactly. My FTDNA test was 2013, Ancestry in late 2015, and 23&Me in early 2018.
I hope you’ll evaluate this new study: https://www.nature.com/articles/s41586-020-03065-y
I have been checking my family’s results at 23andme today. V3 and V4 test this SNP but the more recent test, V5, does not
The new study (that you’ve referenced) downplays the role of blood type, so you should feel some relief from that.
In the actual paper, for rs10490770, it says REF=T and ALT/RISK=C. What do those column headings mean exactly?
The peer-reviewed study says the blood type is a risk factor, though it can’t quantify it. As for the new study, the protective (neutral) value is T; the alternative risk factor is C. So TT = no known elevated risk, CC = identified as elevated risk, CT = some elevated risk.
As a fellow A, i share your concern.
I also have blood type A. From my 23andme data, I see:
rs10490770 3 45864732 TT
so maybe I don’t need to worry as much (I hope)?
The TT is good. The Type A may give you a somewhat higher risk than if you were say type O but with the TT you’re at lower risk than I am!
I could not follow your discussion until I realized that what the paper found was that the highest risk for respiratory failure was for rs 11385942 (A), but this is not present on the direct-to-consumer chips. However, rs 10490770 (C) corresponds 99% of the time for Caucasians with rs 11385942 (A). That is why you were showing a figure that is a combination of the rs 10490770 text and the rs 11385942 graphic. My result is also a (C,T), but my wife has a (T,T). I am the one who should be most concerned.
I have type A blood and have done the Ancestry DNA test but I have no idea how to go further. Is there a possibility that you could explain how to obtain the Covid results from an Ancestry test in an upcoming blog post? This is so interesting but I just can’t figure out how to obtain results for myself .
To Download your Ancestry raw data.
The resulting file is called AncestryDNA.txt. Open that file in any text editor. Then search within it for the value rs10490770.
It will appear on a line that reads something like:
rs10490770 3 45864732 T T (good, no increased COVID risk) OR
rs10490770 3 45864732 C T (not so good, some increased risk) OR
rs10490770 3 45864732 C C (worst of the three, some more increased risk)
Keep in mind, nobody knows how big the increased risk is — just that there’s some greater risk.
Whew! TT and type O blood. Thanks for posting about this. Will be interesting to see where the research goes from this basic starting point.
Now, don’t go thinking you’re immune because of that — it just means you don’t have this one elevated risk, not that you’re always going to be fine.
It’s well worth reading this critique of the Neanderthal paper from John Hawks who is a well respected paleoanthropologist. We still have a lot to learn.
https://medium.com/@johnhawks/neanderthals-and-covid-19-beyond-the-hype-c258dc8bc2c9
Thanks, Judy, for interesting information.
I have the same blood type and CT alleles as you. I find the genetics of all this interesting but not surprising.
Any way of getting to this marker? https://www.ancestry.com/corporate/newsroom/press-releases/ancestry%C2%AE-covid-19-study-points-gene-associated-male-susceptibility-covid-19
I don’t see it in any of my raw tests. You might have to have done the health test with Ancestry. But I’d check with them first.
Judy, would be nice to have an update on this topic based on this article https://www.nature.com/articles/s41586-021-03767-x