4 ms·

they re probably not sequencing asymptomatic people's virus, it would require some specific expedition. it doesn't even sound hard or expensive reply to @ajros

they re probably not sequencing asymptomatic people's virus, it would require some specific expedition. it doesn't even sound hard or expensive reply to @ajross: how would they know someone is asymptomatic? afaik they are mostly testing people who have symptoms , and their contacts (who will have contracted the same , symptomatic strain) I think in germany they did antibody testing, or PCR of swabs of people who mostly no longer had a live virus infection to sequence. also, it seems the idea has merit; and i havent read about any team looking for this specific method (identify gene deletions and tracing). It certainly doesn't hurt (and doesnt cost much) to try btw sweden is doing a survey of live infections in stockholm, however i don't think that they sequence the viruses to @danieltillet: maybe post about it in reddit on r/covid19, some epidemiologists hang out there for the latest news

ajross 6y ago
Are they not? That seems like a pretty obvious experiment to do. For reference: I have a family member in virology. He reports that everyone he knows is now working on covid, mostly because if they don't they can't come to work on anything. The biggest problem is finding subjects that will produce a paper of any kind. I really don't think research bandwidth is the issue here. I guess I have to repeat the question as its converse: is there any evidence that this is not happening? If it isn't, let's figure out the right people to pressure and not just discuss it on HN. And if it is, maybe we should let the experts do their work without pretending to have had their ideas for them?
- danieltillett 6y ago
  If you know anyone working on my idea please let me know as I will update my blog post. Nothing would please me more than to learn that someone is already doing this on a serious level.
danieltillett 6y ago
It is not hard to do the sequencing to find candidate attenuated strains (you are just looking for strains with deletions in key genes). The more difficult part is all the contact tracing in the area around where the strain is first found to check if the strain really is attenuated. The ideal outcome is you find a strain with a deletion and you then test everyone in the area and you find 10,000 more people infected with the strain that have only a mild case and none of these people are in the hospitals. This strain would be very valuable to have.
ajross 6y ago
> how would they know someone is asymptomatic? afaik they are mostly testing people who have symptoms There was literally a paper published yesterday (or the day before) on a blanket screen done on a population in germany to get some data on the undercount of asymptomatic cases. It was front page news on all the mainstream news sites... I gotta be honest. This whole discussion has an "amateur hour" vibe. I have a hard time believing that professional academics in a long-established and very competetive field really failed to remember how the measles vaccine worked. It's not that I think this is a bad idea, just that (1) it's almost certainly someone else's idea already, (2) is therefore probably harder to do than presented and (3) is thus not the magic bullet people are looking for. To wit: stay the fuck home. Maybe someone will save us. They probably won't. We beat this with isolation or we wait for a vaccine.
- danieltillett 6y ago
  I think what you are missing here is what is the novel part of my idea and what is the conventional. It is not novel to think of an attenuated vaccine, what is novel is to look for an attenuated strain in a pandemic using genome sequencing. I hope someone else has thought of this, but so far I haven’t seen any evidence of this. Waiting for vaccine is not a good option. This is a situation with only hard choices.
  - thawaway1837 6y ago
    Why else are hundreds of different labs around the world genome sequencing?
    - danieltillett 6y ago
      To assess the diversity and spread of the virus it appears. To the best of my knowledge nobody is systematically looking for a natural attenuated strain by genome sequencing. If you are then please get in contact with me.
  - ajross 6y ago
    "Waiting for a vaccine" is mostly a strawman. We're being asked to wait 2-3 months for the outbreaks to reach a size where they can be contained by testing, tracing and quarantine. But that only works if people take this seriously and honor the lockdowns.

ajross 6y ago

Are they not? That seems like a pretty obvious experiment to do. For reference: I have a family member in virology. He reports that everyone he knows is now working on covid, mostly because if they don't they can't come to work on anything. The biggest problem is finding subjects that will produce a paper of any kind. I really don't think research bandwidth is the issue here. I guess I have to repeat the question as its converse: is there any evidence that this is not happening? If it isn't, let's figure out the right people to pressure and not just discuss it on HN. And if it is, maybe we should let the experts do their work without pretending to have had their ideas for them?

danieltillett 6y ago
If you know anyone working on my idea please let me know as I will update my blog post. Nothing would please me more than to learn that someone is already doing this on a serious level.

danieltillett 6y ago

It is not hard to do the sequencing to find candidate attenuated strains (you are just looking for strains with deletions in key genes). The more difficult part is all the contact tracing in the area around where the strain is first found to check if the strain really is attenuated. The ideal outcome is you find a strain with a deletion and you then test everyone in the area and you find 10,000 more people infected with the strain that have only a mild case and none of these people are in the hospitals. This strain would be very valuable to have.

ajross 6y ago

> how would they know someone is asymptomatic? afaik they are mostly testing people who have symptoms There was literally a paper published yesterday (or the day before) on a blanket screen done on a population in germany to get some data on the undercount of asymptomatic cases. It was front page news on all the mainstream news sites... I gotta be honest. This whole discussion has an "amateur hour" vibe. I have a hard time believing that professional academics in a long-established and very competetive field really failed to remember how the measles vaccine worked. It's not that I think this is a bad idea, just that (1) it's almost certainly someone else's idea already, (2) is therefore probably harder to do than presented and (3) is thus not the magic bullet people are looking for. To wit: stay the fuck home. Maybe someone will save us. They probably won't. We beat this with isolation or we wait for a vaccine.

danieltillett 6y ago
I think what you are missing here is what is the novel part of my idea and what is the conventional. It is not novel to think of an attenuated vaccine, what is novel is to look for an attenuated strain in a pandemic using genome sequencing. I hope someone else has thought of this, but so far I haven’t seen any evidence of this. Waiting for vaccine is not a good option. This is a situation with only hard choices.
- thawaway1837 6y ago
  Why else are hundreds of different labs around the world genome sequencing?
  - danieltillett 6y ago
    To assess the diversity and spread of the virus it appears. To the best of my knowledge nobody is systematically looking for a natural attenuated strain by genome sequencing. If you are then please get in contact with me.
- ajross 6y ago
  "Waiting for a vaccine" is mostly a strawman. We're being asked to wait 2-3 months for the outbreaks to reach a size where they can be contained by testing, tracing and quarantine. But that only works if people take this seriously and honor the lockdowns.