Thank you for that very detailed reply Jeff, I learnt a lot about how to think about costing this.
The easiest way to collect a pooled sample is the walk around some building and sample everyone. This gets you a big sample pretty cheaply, but it’s not a great one if you want to understand the containing city because it’s likely that many people in the building will get sick on a similar timeframe.
I agree this is true for an office block, but I would think you can do much better without much cost. For example, if you use a high-traffic commuter train station or supermarket I would guess you get a fairly broad cross-section of the city. They’d be somewhat uncorrelated (different home locations with children at different schools, different offices etc.) although obviously the geographical component is still there. Perhaps similar to wastewater though? You could do multiple locations as well though.
It seems like you ought to be able to get down to more like $2/person in which case a pool of 1k costs you $2k in collection. Then add in $1k for sequencing and you’re still well above wastewater.
These numbers are maybe optimistic, but not ridiculously so.
Very likey overestimated upper bound though because that is a proper random sample of the whole population, with ~9.5m of the swabs collected by study workers going to houses. I think this budget might exclude the cost of PCR testing (done individually, not pooled) and a lot of time spent running / analysing the data.
if you use a high-traffic commuter train station or supermarket I would guess you get a fairly broad cross-section of the city
Definitely! Right after writing to you I started thinking about this, estimating costs, and talking to coworkers; sorry for not posting back! I do think something along these lines could work well.
These numbers are maybe optimistic, but not ridiculously so.
My main update since then is that if you do it at a transit station you probably need to compensate people, but also that a small amount of compensation doesn’t sink this. Giving people $5 or a candy bar for a swab is possible, and if a team of two people at a busy transit station can get 50-200 swabs in an hour that’s your biggest sample acquisition cost. I still think $1k is practical for the sequencing.
I’m trying to come up with examples of people doing something similar, which we’d want for presenting this to the IRB. Two examples so far:
Various companies that sample for bone marrow compatibility testing (ex: Be The Match)
Do you know of anything else that feels similar to this? People in public areas collecting biological samples from volunteers (perhaps lightly compensated).
Do you know of anything else that feels similar to this? People in public areas collecting biological samples from volunteers (perhaps lightly compensated).
Afraid not. The closest I can think of is collecting samples from healthy volunteers without any benefit to them, but not in public areas. In particular, I’m thinking of swabbing in primary health settings (eg RGCP/UKHSA run something like this in England, I can’t remember if it only includes those with respiratory symptoms) and testing blood donations (normally serological testing looking for antibodies). REACT (run by Imperial College) did swabbing for COVID via postal recruitment.
A bit of an aside, so maybe not of interest, however, this made me think of serological testing of residual blood samples. That is, when blood is collected for testing (for any clinical reason), not all of it is used in the tests, and the remaining (residual) part is tested. Here, there are no sample collection costs (the blood was collected anyway). However, it doesn’t map exactly because you don’t swab people without respiratory suspicion but you might take blood (eg anemia). Maybe there is an opportunity for either testing blood samples for pathogens (but I have no idea what that looks like) or samples taken for other respiratory reasons (but then you need to think about co-infection, ie does infection with influenza make you less likely to have another respiratory infection).
Finally, some shameless self-promotion. I’m currently nearing PhD competition with nothing lined up. If there are projects looking at these sorts of questions interested in modelling / stats / epidemiology input I’d be very interested, please DM. Please ignore this if unappreciated.
Thank you for that very detailed reply Jeff, I learnt a lot about how to think about costing this.
I agree this is true for an office block, but I would think you can do much better without much cost. For example, if you use a high-traffic commuter train station or supermarket I would guess you get a fairly broad cross-section of the city. They’d be somewhat uncorrelated (different home locations with children at different schools, different offices etc.) although obviously the geographical component is still there. Perhaps similar to wastewater though? You could do multiple locations as well though.
These numbers are maybe optimistic, but not ridiculously so.
The Coronavirus Infection Survey (big UK study which I’ve worked on) cost ~£1b for ~11.5m swabs (Excel sheets with data from Mar 2023 and historical data). Works out as ~$100 / swab.
Very likey overestimated upper bound though because that is a proper random sample of the whole population, with ~9.5m of the swabs collected by study workers going to houses. I think this budget might exclude the cost of PCR testing (done individually, not pooled) and a lot of time spent running / analysing the data.
Definitely! Right after writing to you I started thinking about this, estimating costs, and talking to coworkers; sorry for not posting back! I do think something along these lines could work well.
My main update since then is that if you do it at a transit station you probably need to compensate people, but also that a small amount of compensation doesn’t sink this. Giving people $5 or a candy bar for a swab is possible, and if a team of two people at a busy transit station can get 50-200 swabs in an hour that’s your biggest sample acquisition cost. I still think $1k is practical for the sequencing.
I’m trying to come up with examples of people doing something similar, which we’d want for presenting this to the IRB. Two examples so far:
XpresCheck for COVID tracking at airports (site, [consent brochure] (https://www.xprescheck.com/xpresresources/CDC_COVID_Testing_Brochure.pdf))
Various companies that sample for bone marrow compatibility testing (ex: Be The Match)
Do you know of anything else that feels similar to this? People in public areas collecting biological samples from volunteers (perhaps lightly compensated).
Afraid not. The closest I can think of is collecting samples from healthy volunteers without any benefit to them, but not in public areas. In particular, I’m thinking of swabbing in primary health settings (eg RGCP/UKHSA run something like this in England, I can’t remember if it only includes those with respiratory symptoms) and testing blood donations (normally serological testing looking for antibodies). REACT (run by Imperial College) did swabbing for COVID via postal recruitment.
A bit of an aside, so maybe not of interest, however, this made me think of serological testing of residual blood samples. That is, when blood is collected for testing (for any clinical reason), not all of it is used in the tests, and the remaining (residual) part is tested. Here, there are no sample collection costs (the blood was collected anyway). However, it doesn’t map exactly because you don’t swab people without respiratory suspicion but you might take blood (eg anemia). Maybe there is an opportunity for either testing blood samples for pathogens (but I have no idea what that looks like) or samples taken for other respiratory reasons (but then you need to think about co-infection, ie does infection with influenza make you less likely to have another respiratory infection).
Finally, some shameless self-promotion. I’m currently nearing PhD competition with nothing lined up. If there are projects looking at these sorts of questions interested in modelling / stats / epidemiology input I’d be very interested, please DM. Please ignore this if unappreciated.