Genome wide SNP analysis in COVID-19 susceptibility..

4,597 Views | 34 Replies | Last: 4 yr ago by culdeus
Marcus Aurelius
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AG
https://www.nejm.org/doi/full/10.1056/NEJMoa2020283?query=featured_home

Interesting study from Spain, Italy 1980 COVID-19 pts. Genome wide 8,582,968 single-nucleotide polymorphisms (SNP) genotype analysis. Compared to control group. 2 loci statistically significant allele variants: 3p21.31 which encodes SLC6A20, LZTFL1, CCR9, FYCO1, CXCR6, and XCR1 genes. They express proteins highly found in lung tissue. The allele variant led to varying levels of expression of these genes. The other SNP loci variant was 9q34.2, which very interestingly is the ABO system chromosomal region. They found a protective effect of group O and harmful effect of group A.

This helps explain heterogeneity in COVID-19 severity from person to person.
Windy City Ag
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AG
KlinkerAg11
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I'd assume this is why there are so many people with no symptoms.
Marcus Aurelius
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Probably more to it but yes.
Marcus Aurelius
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BTW - SNPs are subtle differences in nucleotide sequences which alter proteins slightly. They are not considered to be "mutations" as most don't confer major deleterious physiologic effects. With the entire human genome published there is a massive database for these SNPs. You can analyze massive size high thru put samples using array technology. Like in this study over 8 million SNPs assayed.
RVAg02
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Can someone explain this to me like I'm 4?
Windy City Ag
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The way I read it is they studied the genome of 1,890 patients across a few countries . . . . two genetic variants jumped out as statistically significant, or turning up a whole lot more in the patients that were really ill.

This is cool because it both explains why some folks get violently ill or die and others just think they have allergies. It also might help us figure out in advance who is more at risk and we can lock those people away and get back to our daily business.

Marcus Aurelius
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ClickClackAg31
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ClickClackAg31
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What RVAg said.



(Windy's explanation makes sense though, just wanted to post the gif)

Is it possible these more dangerous "versions" are dying out and only the more milder strains are surviving? This would explain the drastic fall off of deaths worldwide that doesnt follow the case reduction rate despite more testing...
Fitch
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RVAg02 said:

Can someone explain this to me like I'm 4?
Blood types matter. Type O fare better. Type A, be wary.
Marcus Aurelius
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And the differences in these structural lung proteins. The statistical significance in these two loci variants was huge - for those statistic fans, P values as low 1.15 x 10 to the minus 10 (can't type upper score on here).
Windy City Ag
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Quote:

or those statistic fans, P values as low 1.15 x 10 to the minus 10 (can't type upper score on here).
I always wondered why the T stat was not good enough. Why did they have to go and add the P Value?
AggieSarah01
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Is there an easy way to find out who has the lung proteins that make you more susceptible to severe disease?
plain_o_llama
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Marcus,

If they had a test to detect these variants would it change treatments any? Slower or faster to admit to the hospital?
Diyala Nick
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As a decision tree in clinical treatment, would it be

>If positive,
>Then test for specific variation,
>If positive for variation,
>Then immediately begin Remdesevir

???

Give the best known antiviral as early as possible in the course of the disease to those genetically most at risk?
Marcus Aurelius
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AggieSarah01 said:

Is there an easy way to find out who has the lung proteins that make you more susceptible to severe disease?
Not now. But the cool thing is now researchers can focus on these proteins to elucidate the mechanisms of disease more.
Fitch
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Thanks. Just chiming in from hour 5 of my conference call...didn't take the time to read it all.
Marcus Aurelius
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plain_o_llama said:

Marcus,

If they had a test to detect these variants would it change treatments any? Slower or faster to admit to the hospital?

Just talking about this. For now - I think the only clinical decision impact this research offers is ABO. I would like to serotype all COVID admits. Type A pts - you're more vigilant for severe disease. Pull the trigger on the effective drugs earlier. Type O pts - maybe be able to admit less. Discharge sooner.
AggieYankee1
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Serious question - what does age have to do with blood type. In the results it was all 50 years old+ but nothing about young's.

My husband is 35 - good health - double vaccinated (military life) but type A is at a high risk job. Does Type A mean a coMorbid
Now?

Do I need to tell him to look for other work?
Keegan99
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Excellent. Thank you for sharing!
Marcus Aurelius
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AggieYankee1 said:

Serious question - what does age have to do with blood type. In the results it was all 50 years old+ but nothing about young's.

My husband is 35 - good health - double vaccinated (military life) but type A is at a high risk job. Does Type A mean a coMorbid
Now?

Do I need to tell him to look for other work?
ABO is a congenital trait, thus age has no bearing. I would say he should just be more vigilant with standard precautions and don't seek a new job.
AggieYankee1
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Thank you.
RVAg02
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ok, I was finally getting around to not being so worried about this and now this.

I'm 39 in good health, but type A blood. Up until now, I thought blood type was just another factor in the whole thing, but was outweighed by age and co-morbs.

BiochemAg97
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RVAg02 said:

ok, I was finally getting around to not being so worried about this and now this.

I'm 39 in good health, but type A blood. Up until now, I thought blood type was just another factor in the whole thing, but was outweighed by age and co-morbs.


Probably still is.

Age and co-morbs has a strong correlation. If the genetic markers were the dominate factor, we wouldn't see age dependence or the heavy % of co-morbid as these genetic markers would be distributed across the population (genetic markers like this don't change with age).
Marcus Aurelius
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RVAg02 said:

ok, I was finally getting around to not being so worried about this and now this.

I'm 39 in good health, but type A blood. Up until now, I thought blood type was just another factor in the whole thing, but was outweighed by age and co-morbs.


By all means don't construe this paper as meaning these genetic factors are solely driving the disease severity. Just another clue to the mystery. The obvious clinical comorbidities, age etc play a large role.
RVAg02
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I'm off the ledge. Thanks.
Marcus Aurelius
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"On chromosome 3p21.31, the peak association signal covered a cluster of six genes (SLC6A20, LZTFL1, CCR9, FYCO1, CXCR6, and XCR1), several of which have functions that are potentially relevant to Covid-19. A causative gene cannot be reliably implicated by the present data. One candidate is SLC6A20, which encodes the sodiumimino acid (proline) transporter 1 (SIT1) and which functionally interacts with angiotensin-converting enzyme 2, the SARS-CoV-2 cell-surface receptor.28,29 However, the locus also contains genes encoding chemokine receptors, including the CC motif chemokine receptor 9 (CCR9) and the C-X-C motif chemokine receptor 6 (CXCR6), the latter of which regulates the specific location of lung-resident memory CD8 T cells throughout the sustained immune response to airway pathogens, including influenza viruses.30 Flanking genes (e.g., CCR1 and CCR2) also have relevant functions,31 and further studies will be needed to delineate the functional consequences of detected associations."

"Our genetic data confirm that blood group O is associated with a risk of acquiring Covid-19 that was lower than that in non-O blood groups, whereas blood group A was associated with a higher risk than non-A blood groups.33,34 The biologic mechanisms undergirding these findings may have to do with the ABO group per se (e.g., with the development of neutralizing antibodies against protein-linked N-glycans)36 or with other biologic effects of the identified variant,37-39 including the stabilization of von Willebrand factor.40,41"

For those molecular biology types that want to delve into this deeper. Fascinating stuff. Makes sense. ABO's effect on von Willebrand factor can explain the hypercoaguable state in COVID-19. More reason to serotype these patients. Type A patients need anticoagulation from admission.
AggieYankee1
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Ok final question Doc ...

Does him being type A put him in the same area of some who is older and has comorbids.

I have read about the results from the Roosevelt and understanding that logically some of them had to be type a and young and hardly any of them got sick except for that one man (God Rest His Soul).

My husband was also vaccinated out the ass cause of his length of service and including when he was a kid. Thankfully his mom is nuts and kept a record of all his doctor visits.

I asked my doctor about this and just shrugged at him on the video and said... you and him are young and healthy... I would ignore the study for your age group and health.

I'm not holding you to this but I would like to try and learn more for my husband.
Marcus Aurelius
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Yet to be determined. I would say if he were 350 #s, with diabetes, CAD, HTN and chronic renal insufficiency I would be worried. Those factors are much more important. He's young and sounds to be in badass military shape. Even with type A blood his risk of dying from COVID-19 is low. Think your man is good.
flyingaggie12
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I'm sorry for my ignorance but what does this mean for people who are neither type A or type O but B and AB?Do they just lie somewhere in the middle?
Marcus Aurelius
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Good ? Type B seems to not affect susceptibility. AB ? Not sure remains to be seen. But I would expect some increased risk.
puryear94
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Is there a difference in having AO versus AA? I have A, but my son has O which means I have to be AO.
Marcus Aurelius
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Good ? Not sure. Story untold for heterozygotes. Especially AO.
Reveille
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Marcus Aurelius said:

https://www.nejm.org/doi/full/10.1056/NEJMoa2020283?query=featured_home

Interesting study from Spain, Italy 1980 COVID-19 pts. Genome wide 8,582,968 single-nucleotide polymorphisms (SNP) genotype analysis. Compared to control group. 2 loci statistically significant allele variants: 3p21.31 which encodes SLC6A20, LZTFL1, CCR9, FYCO1, CXCR6, and XCR1 genes. They express proteins highly found in lung tissue. The allele variant led to varying levels of expression of these genes. The other SNP loci variant was 9q34.2, which very interestingly is the ABO system chromosomal region. They found a protective effect of group O and harmful effect of group A.

This helps explain heterogeneity in COVID-19 severity from person to person.
Thanks for posting! More evidence on the severity per blood types. I think getting blood types on patients is definitely something to start considering now that their growing evidence that it plays a role in those with severe disease.
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