jefftk

Software engineer at the Nucleic Acid Observatory in Boston. Speaking for myself unless I say otherwise.

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jefftk20

I would expect that to work fine as an adult on my own, but if I'm the one who gets to the street first it would be confusing to my kids.

jefftk40

We are eating food cooked at home, which is a lot cheaper then frozen meals and much cheaper than restaurant food. We have a dinner rotation with housemates (and a neighbor) where we take turns cooking dinner, so Julia and I each usually cook once a week.

What I cooked last night:

  • 3lb sausages, bought on sale @ $2/lb
    • I often buy meat on sale and keep it in our chest freezer
  • 2lb pasta @ $1.20/lb
  • 2lb tomatoes @ $2/lb
  • 2lb onions @ $2/lb
  • 2 bell peppers @ $2/each

Usually there'd also be a vegan or vegetarian option, but we didn't happen to have anyone who needed that any last night. If we did I probably would have baked some tofu, 1lb @ $3.50/lb.

Overall cost, assuming I'd included the tofu, is ~$25 when you count the small amount of amortized spices, cooking oil, etc. This would be dinner for about 10 people, and several lunches. About $2/meal. $732 is ~$5/person/day, and lunch and breakfast are generally much lighter and cheaper than dinner.

My lunch is also provided by my work, and once a week we have dinner with my extended family at my dad's house. I'm also not counting the electricity used to run the stove, but I think that's probably too small to matter?

A much larger missing expense is the opportunity cost of each adult's time cooking, but I can combine cooking with watching the kids to some extent and it's also something we enjoy.

jefftk20

I only use this setup when I'm away from my desk. If I'm in a convenient location I can just plug into an external monitor at the right height.

jefftk20

(somehow) make bread that was likely to last longer

You could decrease the water content and not leaven it, making it into hardtack. This will last for years if kept dry. But it's very unpleasant to eat, and I don't think people would buy it or bakers would make it unless required to.

jefftk20

Whoops; fixed!

jefftk51

I think it's most likely contamination within the lab doing the nucleic acid extraction, since talking to them they do work with lentiviral vectors.

jefftk20

Setting aside economics or technology, would it in principle be possible to detect a variant of concern in flight and quarantine the passengers until further testing could be done?

There are two pretty different scenarios:

  1. Initial detection: if you don't already know whether there's something out there, you'll need to do metagenomic sequencing or something similar to identify the pathogen. This is the part of the problem that the NAO is trying to solve. While I haven't looked into the absolute-minimum-sequencing-time portion of the space deeply, my understanding is if you want a reasonable cost-per read you need to use a sequencing method that (counting both the preparation and the sequencing machine running) takes multiple days. So not a good fit for per-flight testing.

  2. Containment: we've learned about a pathogen somehow (ex: someone with unusual symptoms, metagenomic sequencing) and we're trying to keep it from spreading. Now we can use a targeted method, such as qPCR, where there are stand-alone speed-optimized options here that take under an hour (ex: KrakenSense). In this case, the question is, how do you get the samples to test? Ideally you'd get everyone to give a sample before boarding, which you could do a pooled test on while the plane was in flight, but that requires infrastructure and cooperation with the originating country.

you're saying that your prelim results show that 0.2% of the sampled population would need to have at some point in the past been infected for the variant of concern to be detectable?

That's correct. While detection is fundamentally based on the people who are currently shedding copies of the virus, but our modeling counts "time" in terms of the progress of the infection through the population.

jefftk20

suggesting this would be deployed in airports rather than municipalities. So the plan has changed?

We're also exploring arport monitoring, but airplane blackwater tanks not terminals. Preliminary data from pooled tank samples (you collect between the truck that sucks it out of the planes and the dumping point) looks very good.

infected travelers/day in an airport setting to get .2% of the wastewater being from them

Sorry to keep harping in this, but 0.2% of wastewater from people who've ever been infected (cumulative incidence) not currently infected (prevalence). While shedding is primarily about prevalence (though varying over the course of the infection) for evaluating a system we generally think cumulative incidence is more informative because it tells you much more and how far along the pandemic is.

jefftk20

Technically it's 0.2% cumulative incidence not 0.2% prevalence, but depending on the assumptions you make about how long infections last and how quickly they spread they're usually in the same ballpark.

Many SeaTac travelers do not defecate, so your effective sample size is smaller. Possibly too small for this to work well. This modeling is generally assuming larger sewersheds, like municipalities.

jefftk50

if someone modified a virus that NAO wasn't explicitly monitoring for modifications, then that would go undetected?

That's correct. But it's extremely cheap to monitor an additional virus, so there's not much downside to casting a large net.

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