4 ms·

I posted/read this article, because I (1) have worked a bit with genomic data and I can read their papers and (2) I have full genome sequenced my family. The p

I posted/read this article, because I (1) have worked a bit with genomic data and I can read their papers and (2) I have full genome sequenced my family. The paper implicates the ACE2 gene that encodes a protein that acts as a receptor for covid-19 (and SARS) - based on studies showing the correlation of SARS infection with ACE2 expression. The paper investigates which mutations (variants) in human genomes could lead to lower expression of ACE2 (lower activity levels of the gene, meaning less receptors for covid-19). However, in China, there weren't that many: "These data suggested that there was a lack of natural resistant mutations for coronavirus S-protein binding in populations." 32 candidate variants are identified, so if you have done whole genome sequencing of your DNA, you can get some very rough estimate of your suspectability to acquiring covid-19 - if you have a mutation or two there. Naturally sub-saharan Africans have higher genomic diversity, so there's probably more protective mutations in their population.

mquander 7y ago
Sorry for the small derail, but can you comment on your decision to sequence your family? I considered doing this recently but it wasn't clear to me that I would obtain much actionable information, so I declined to expend the effort. (After all, it will only get cheaper and easier.)
- jamesblonde 7y ago
  I will check to see if we have many of the ACE variants defined in the paper to get an idea of where we stand. Although it is still just probabilities, it might mean the difference between moving to the summer house for 6 months with them or staying in the city. I could work remote, so that's a possibility.
DoreenMichele 7y ago
I'm just a lay person. Would you be able to say anything (or point me to anything) about the relationship between ACE2 and the CFTR? The only thing I've found so far is this: https://bmcpulmmed.biomedcentral.com/articles/10.1186/1471-2466-12-41 https://bmcpulmmed.biomedcentral.com/articles/10.1186/1471-2... The CF community seems to be assuming this will be very bad for anyone with CF, but the reality is CF exists because it's like Sickle Cell: it's protective against some infections. CF community links: https://www.cfireland.ie/about-cf/latest-news/cfi-update-coronavirus-disease-cov-19 https://www.cfireland.ie/about-cf/latest-news/cfi-update-cor... https://www.reddit.com/r/CysticFibrosis/comments/fb4cz7/the_potential_danger_of_covid19_coronavirus_to/ https://www.reddit.com/r/CysticFibrosis/comments/fb4cz7/the_...
- jamesblonde 7y ago
  Two of my boys have CF, so i have skin in this game. They are young, which is positive. The economist are saying that it is expected that 25-70% of people globally will get infected, so i am worried. But I haven't found out anything yet.
  - deleted 7y ago
    [deleted]
- ekelsen 7y ago
  What infections does having one copy of the CF gene protect against? The wikipedia page suggests this is an unproven hypothesis.
  - DoreenMichele 7y ago
    Research suggests cholera and tuberculosis. First-hand experience suggests it protects against Winter Vomiting, a deadly flu that went around years ago.
    - ekelsen 7y ago
      I can't find any studies that confirm cholera or tuberculosis. Do you have any citations? For example, I found: https://www.ncbi.nlm.nih.gov/pubmed/26527495 https://www.ncbi.nlm.nih.gov/pubmed/26527495 which is a single author hypothesis.
      - DoreenMichele 7y ago
        Sorry, no. I haven't been on a CF list in many years. I'm aware that it's just a hypothesis that it protects against cholera and tuberculosis. My confidence that it protects against some things is based primarily on first-hand experience. I and my oldest son both have a form of CF. About 18 years ago, not long after we were diagnosed, my other son came down with Winter Vomiting. It was a particularly deadly flu. He spent 8 days laying in bed, mostly not eating. I told him at some point that if he became too dehydrated, I would take him to the ER for an IV. He had an IV once before and didn't want another one. So once a day, he would eat a few crackers or some ramen and drink about 32 ounces of water and promptly projectile vomit everything back up. He was utterly miserable for more than a week. Meanwhile, I and my oldest son felt sort of blah for maybe a day and a half. We routinely felt blah. That's entirely normal given our genetic disorder. We would have never known we had been exposed to Winter Vomiting had my other son not been so horrendously sick with it. So that's the primary basis of my opinion that it's like Sickle Cell and is more common in some populations due to being protective against some things that, historically, those populations were exposed to a great deal. I'm not trying to convince you of anything. I'm only explaining why I think it makes sense. You will need to decide for yourself what makes sense to you and what kind of research is adequately compelling to convince you of a thing. Please don't turn this into some weird thing where you feel some need to follow me around from conversation to conversation and harangue me and prove me wrong and so forth. Far too many internet strangers have done things like that to me. I was commenting here in hopes of more accurately assessing risks for me and my sons, not in hopes of convincing the world to see things X way. You aren't required to agree with me. By the same token, I'm not required to agree with you. Good luck in finding answers that adequately satisfy you. But I can't really help you with that.
JPLeRouzic 7y ago
Thanks, Does this implies somehow that people with high blood pressure are more at risk of covid-19 infection?
- jamesblonde 7y ago
  No, it says nothing about blood pressure. It is about which genetic variants you have that determine the level of angiotensin-converting enzyme-2 in your body. If you have more of it, you probably have a higher chance of acquiring corona-viruses.
fouc 7y ago
Higher genomic diversity is just another way of saying there's more ethnic groups in Africa, right? So it's not particularly a racial thing.
- afiori 7y ago
  if I remember correctly from a genetic perspective the group of "not African ethnicities" is more uniform than the group of "African ethnicities"
- xiphias2 7y ago
  It's a historical thing: humans were evolving for much longer time in Africa than in other continents.
  - username90 7y ago
    All humans have evolved for the same amount of time. It is just that a smaller part of the population decided to emigrate than to stay a long time ago.
    - bonzini 7y ago
      Migration causes a genetic bottleneck that (sort of) resets the counter.
      - bobmaxup 7y ago
        Is there a term for this?
        lordnacho 7y ago
        Perhaps Founder Effect is what you are after?
    - afiori 7y ago
      yes, but for much longer in Africa than outside of Africa. If you assume that "diversity" increases mostly steadily over time* then there is much more diversity in Africa than in the rest of the world. * diversity is quite different from evolution

mquander 7y ago

Sorry for the small derail, but can you comment on your decision to sequence your family? I considered doing this recently but it wasn't clear to me that I would obtain much actionable information, so I declined to expend the effort. (After all, it will only get cheaper and easier.)

jamesblonde 7y ago
I will check to see if we have many of the ACE variants defined in the paper to get an idea of where we stand. Although it is still just probabilities, it might mean the difference between moving to the summer house for 6 months with them or staying in the city. I could work remote, so that's a possibility.

DoreenMichele 7y ago

I'm just a lay person. Would you be able to say anything (or point me to anything) about the relationship between ACE2 and the CFTR? The only thing I've found so far is this: https://bmcpulmmed.biomedcentral.com/articles/10.1186/1471-2466-12-41 https://bmcpulmmed.biomedcentral.com/articles/10.1186/1471-2... The CF community seems to be assuming this will be very bad for anyone with CF, but the reality is CF exists because it's like Sickle Cell: it's protective against some infections. CF community links: https://www.cfireland.ie/about-cf/latest-news/cfi-update-coronavirus-disease-cov-19 https://www.cfireland.ie/about-cf/latest-news/cfi-update-cor... https://www.reddit.com/r/CysticFibrosis/comments/fb4cz7/the_potential_danger_of_covid19_coronavirus_to/ https://www.reddit.com/r/CysticFibrosis/comments/fb4cz7/the_...

jamesblonde 7y ago
Two of my boys have CF, so i have skin in this game. They are young, which is positive. The economist are saying that it is expected that 25-70% of people globally will get infected, so i am worried. But I haven't found out anything yet.
- deleted 7y ago
  [deleted]
ekelsen 7y ago
What infections does having one copy of the CF gene protect against? The wikipedia page suggests this is an unproven hypothesis.
- DoreenMichele 7y ago
  Research suggests cholera and tuberculosis. First-hand experience suggests it protects against Winter Vomiting, a deadly flu that went around years ago.
  - ekelsen 7y ago
    I can't find any studies that confirm cholera or tuberculosis. Do you have any citations? For example, I found: https://www.ncbi.nlm.nih.gov/pubmed/26527495 https://www.ncbi.nlm.nih.gov/pubmed/26527495 which is a single author hypothesis.
    - DoreenMichele 7y ago
      Sorry, no. I haven't been on a CF list in many years. I'm aware that it's just a hypothesis that it protects against cholera and tuberculosis. My confidence that it protects against some things is based primarily on first-hand experience. I and my oldest son both have a form of CF. About 18 years ago, not long after we were diagnosed, my other son came down with Winter Vomiting. It was a particularly deadly flu. He spent 8 days laying in bed, mostly not eating. I told him at some point that if he became too dehydrated, I would take him to the ER for an IV. He had an IV once before and didn't want another one. So once a day, he would eat a few crackers or some ramen and drink about 32 ounces of water and promptly projectile vomit everything back up. He was utterly miserable for more than a week. Meanwhile, I and my oldest son felt sort of blah for maybe a day and a half. We routinely felt blah. That's entirely normal given our genetic disorder. We would have never known we had been exposed to Winter Vomiting had my other son not been so horrendously sick with it. So that's the primary basis of my opinion that it's like Sickle Cell and is more common in some populations due to being protective against some things that, historically, those populations were exposed to a great deal. I'm not trying to convince you of anything. I'm only explaining why I think it makes sense. You will need to decide for yourself what makes sense to you and what kind of research is adequately compelling to convince you of a thing. Please don't turn this into some weird thing where you feel some need to follow me around from conversation to conversation and harangue me and prove me wrong and so forth. Far too many internet strangers have done things like that to me. I was commenting here in hopes of more accurately assessing risks for me and my sons, not in hopes of convincing the world to see things X way. You aren't required to agree with me. By the same token, I'm not required to agree with you. Good luck in finding answers that adequately satisfy you. But I can't really help you with that.

JPLeRouzic 7y ago

Thanks, Does this implies somehow that people with high blood pressure are more at risk of covid-19 infection?

jamesblonde 7y ago
No, it says nothing about blood pressure. It is about which genetic variants you have that determine the level of angiotensin-converting enzyme-2 in your body. If you have more of it, you probably have a higher chance of acquiring corona-viruses.

fouc 7y ago

Higher genomic diversity is just another way of saying there's more ethnic groups in Africa, right? So it's not particularly a racial thing.

afiori 7y ago
if I remember correctly from a genetic perspective the group of "not African ethnicities" is more uniform than the group of "African ethnicities"
xiphias2 7y ago
It's a historical thing: humans were evolving for much longer time in Africa than in other continents.
- username90 7y ago
  All humans have evolved for the same amount of time. It is just that a smaller part of the population decided to emigrate than to stay a long time ago.
  - bonzini 7y ago
    Migration causes a genetic bottleneck that (sort of) resets the counter.
    - bobmaxup 7y ago
      Is there a term for this?
      - lordnacho 7y ago
        Perhaps Founder Effect is what you are after?
  - afiori 7y ago
    yes, but for much longer in Africa than outside of Africa. If you assume that "diversity" increases mostly steadily over time* then there is much more diversity in Africa than in the rest of the world. * diversity is quite different from evolution