[math-fun] Contract-tracing virus ('CTV') (was Re: Retrospective contact tracing)
I've been following TWiV (This Week in Virology) ever since March, so I've been musing about various things that could be done with viruses and infections. Also, '60 Minutes' recently had a segment about a very cool technology which uses a CRISPR-like technology to correct the DNA 'SNIP' which causes sickle cell disease. Here are some ideas (please save this email to inoculate the world against someone filing for an invalid patent on these thoughts): 1. Construct a *non-disease* virus that is extremely contagious, and replicates, but doesn't cause any signs, symptoms or disease. However, it includes a certain 'identification sequence' which incorporates a huge amount of redundancy to guard against information loss. This non-disease infection ('NDI') *automatically* does contract tracing, because it is easy to test someone for the 'NDI' and its ID sequence. Possible application: infect everyone who gets on a particular airplane with an flight#-distinguishable NDI, so that one can trace not only everyone who was on the airplane, but also everyone who contacted them in the subsequent weeks. If the NDI is suitably engineered, it shouldn't last in the body longer than a month or so, which provides enough time to do 'contact tracing', but not enough time to be a permanent privacy problem. Risk: what if the NDI mutates into a DI -- i.e., it produces an actual disease? 2. Ditto the above, except that the NDI is actually a non-disease *vaccine*! Getting the NDI inoculates the victim against a real disease. This is a variant on the Salk/Sabin dead/weakened vaccine idea, except that this NDI 'vaccine' can *propagate all by itself*. This idea is analogous to releasing sterile males into a population of bad actor animals so that they no longer reproduce. 3. Ditto the above, but incorporate CRISPR technology to insert data into a host cell's DNA sequence. This version allows for permanent storage. 4. Ditto the above, but with the sickle cell repairer CRISPR-like technology. Everyone can get & transmit this NDI, but only those with sickle cell disease will see an effect -- the elimination of the sickle cell disease. 5. Combine this idea with a Turing-universal set of RNA/DNA CRISPR-like 'transformers'. This enables an arbitrary distributed computation while the virus propagates. At 11:21 AM 8/12/2020, Michael Kleber wrote:
Following up on our discussion in April/May about the non-uniformity in COVID transmission event sizes -- i.e. the average reproduction number R_e doing a bad job of explaining dynamics because the distribution is highly skewed.
Japan's COVID contact tracing (and now Massachusetts's also) are using *retrospective* rather than prospective tracing. In brief, when someone tests positive, the standard prospective approach is to try to track down the people they might have given it to -- their children in the transmission tree. In retrospective tracing, you instead look for their *siblings* in the transmission tree: other people who might have become infected the same time they did.
In a regime where lots of transmission happens at "superspreading events", you get a lot of benefit from this change -- even after you pay the latency cost of trying to find people one infection-generation later in their disease cycle. Here's some analysis of the dynamics:
Twitter thread: https://twitter.com/AdamJKucharski/status/1293472353758871552 Preprint: https://www.medrxiv.org/content/10.1101/2020.08.01.20166595v1.full.pdf
--Michael
FYI, I'll be taking up a collection to fund a Human Subjects Institutional Review Board with the goal of preventing Henry from implementing any of these ideas. On Wed, Aug 12, 2020 at 3:45 PM Henry Baker <hbaker1@pipeline.com> wrote:
I've been following TWiV (This Week in Virology) ever since March, so I've been musing about various things that could be done with viruses and infections.
Also, '60 Minutes' recently had a segment about a very cool technology which uses a CRISPR-like technology to correct the DNA 'SNIP' which causes sickle cell disease.
Here are some ideas (please save this email to inoculate the world against someone filing for an invalid patent on these thoughts):
1. Construct a *non-disease* virus that is extremely contagious, and replicates, but doesn't cause any signs, symptoms or disease. However, it includes a certain 'identification sequence' which incorporates a huge amount of redundancy to guard against information loss.
This non-disease infection ('NDI') *automatically* does contract tracing, because it is easy to test someone for the 'NDI' and its ID sequence.
Possible application: infect everyone who gets on a particular airplane with an flight#-distinguishable NDI, so that one can trace not only everyone who was on the airplane, but also everyone who contacted them in the subsequent weeks.
If the NDI is suitably engineered, it shouldn't last in the body longer than a month or so, which provides enough time to do 'contact tracing', but not enough time to be a permanent privacy problem.
Risk: what if the NDI mutates into a DI -- i.e., it produces an actual disease?
2. Ditto the above, except that the NDI is actually a non-disease *vaccine*! Getting the NDI inoculates the victim against a real disease. This is a variant on the Salk/Sabin dead/weakened vaccine idea, except that this NDI 'vaccine' can *propagate all by itself*.
This idea is analogous to releasing sterile males into a population of bad actor animals so that they no longer reproduce.
3. Ditto the above, but incorporate CRISPR technology to insert data into a host cell's DNA sequence.
This version allows for permanent storage.
4. Ditto the above, but with the sickle cell repairer CRISPR-like technology. Everyone can get & transmit this NDI, but only those with sickle cell disease will see an effect -- the elimination of the sickle cell disease.
5. Combine this idea with a Turing-universal set of RNA/DNA CRISPR-like 'transformers'. This enables an arbitrary distributed computation while the virus propagates.
At 11:21 AM 8/12/2020, Michael Kleber wrote:
Following up on our discussion in April/May about the non-uniformity in COVID transmission event sizes -- i.e. the average reproduction number R_e doing a bad job of explaining dynamics because the distribution is highly skewed.
Japan's COVID contact tracing (and now Massachusetts's also) are using *retrospective* rather than prospective tracing. In brief, when someone tests positive, the standard prospective approach is to try to track down the people they might have given it to -- their children in the transmission tree. In retrospective tracing, you instead look for their *siblings* in the transmission tree: other people who might have become infected the same time they did.
In a regime where lots of transmission happens at "superspreading events", you get a lot of benefit from this change -- even after you pay the latency cost of trying to find people one infection-generation later in their disease cycle. Here's some analysis of the dynamics:
Twitter thread: https://twitter.com/AdamJKucharski/status/1293472353758871552 Preprint: https://www.medrxiv.org/content/10.1101/2020.08.01.20166595v1.full.pdf
--Michael
_______________________________________________ math-fun mailing list math-fun@mailman.xmission.com https://mailman.xmission.com/cgi-bin/mailman/listinfo/math-fun
-- Forewarned is worth an octopus in the bush.
Back in 2001, there were RFID chips the size of bits of glitter: https://www.snopes.com/fact-check/smart-dust/ Now they're small enough to fit into individual cells: https://www.rfidjournal.com/researchers-develop-microscopic-rfid-chip-to-emb... You just need to sprinkle it around and keep track of what ids were sprinkled where. It'll stick to shoes, clothing, hair, etc. When the dust is ubiquitous enough and small enough, we'll be able to reconstruct everywhere a person has been (with an exponentially decaying window over some timescale inversely proportional to the size of the dust) with a simple RF pulse. There may be some cross-contamination from picking up bits of dust that others have dropped, but for contact tracing, that's useful info. In response, people may start taking "EMP showers" to overload and short out the passive RFID dust they picked up that day. On Wed, Aug 12, 2020 at 1:45 PM Henry Baker <hbaker1@pipeline.com> wrote:
I've been following TWiV (This Week in Virology) ever since March, so I've been musing about various things that could be done with viruses and infections.
Also, '60 Minutes' recently had a segment about a very cool technology which uses a CRISPR-like technology to correct the DNA 'SNIP' which causes sickle cell disease.
Here are some ideas (please save this email to inoculate the world against someone filing for an invalid patent on these thoughts):
1. Construct a *non-disease* virus that is extremely contagious, and replicates, but doesn't cause any signs, symptoms or disease. However, it includes a certain 'identification sequence' which incorporates a huge amount of redundancy to guard against information loss.
This non-disease infection ('NDI') *automatically* does contract tracing, because it is easy to test someone for the 'NDI' and its ID sequence.
Possible application: infect everyone who gets on a particular airplane with an flight#-distinguishable NDI, so that one can trace not only everyone who was on the airplane, but also everyone who contacted them in the subsequent weeks.
If the NDI is suitably engineered, it shouldn't last in the body longer than a month or so, which provides enough time to do 'contact tracing', but not enough time to be a permanent privacy problem.
Risk: what if the NDI mutates into a DI -- i.e., it produces an actual disease?
2. Ditto the above, except that the NDI is actually a non-disease *vaccine*! Getting the NDI inoculates the victim against a real disease. This is a variant on the Salk/Sabin dead/weakened vaccine idea, except that this NDI 'vaccine' can *propagate all by itself*.
This idea is analogous to releasing sterile males into a population of bad actor animals so that they no longer reproduce.
3. Ditto the above, but incorporate CRISPR technology to insert data into a host cell's DNA sequence.
This version allows for permanent storage.
4. Ditto the above, but with the sickle cell repairer CRISPR-like technology. Everyone can get & transmit this NDI, but only those with sickle cell disease will see an effect -- the elimination of the sickle cell disease.
5. Combine this idea with a Turing-universal set of RNA/DNA CRISPR-like 'transformers'. This enables an arbitrary distributed computation while the virus propagates.
At 11:21 AM 8/12/2020, Michael Kleber wrote:
Following up on our discussion in April/May about the non-uniformity in COVID transmission event sizes -- i.e. the average reproduction number R_e doing a bad job of explaining dynamics because the distribution is highly skewed.
Japan's COVID contact tracing (and now Massachusetts's also) are using *retrospective* rather than prospective tracing. In brief, when someone tests positive, the standard prospective approach is to try to track down the people they might have given it to -- their children in the transmission tree. In retrospective tracing, you instead look for their *siblings* in the transmission tree: other people who might have become infected the same time they did.
In a regime where lots of transmission happens at "superspreading events", you get a lot of benefit from this change -- even after you pay the latency cost of trying to find people one infection-generation later in their disease cycle. Here's some analysis of the dynamics:
Twitter thread: https://twitter.com/AdamJKucharski/status/1293472353758871552 Preprint: https://www.medrxiv.org/content/10.1101/2020.08.01.20166595v1.full.pdf
--Michael
_______________________________________________ math-fun mailing list math-fun@mailman.xmission.com https://mailman.xmission.com/cgi-bin/mailman/listinfo/math-fun
-- Mike Stay - metaweta@gmail.com http://math.ucr.edu/~mike https://reperiendi.wordpress.com
participants (3)
-
Henry Baker -
Michael Kleber -
Mike Stay