This sounds like a really valuable project, and I’m glad you’re working on it! What sort of end-to-end latency (sample collection to analysis complete) do you think you might be able to achieve? For example, CDC Flu Virologic Surveillance has a latency of ~2 weeks (the most recent is currently from the week ending 2022-04-30, which I think means 12-18d since diagnosis), while MWRA Biobot typically posts data from two days ago each afternoon. If you’re trying to catch things with rapid growth, getting down to a day or lower is probably pretty important?
Yes—and since I did my dissertation partly to ask the question of how valuable it would be to reduce that delay, I feel compelled to note that the CDC’s syndromic surveillance data is at T+2 weeks, which isn’t actually based on diagnosis, but symptoms. The NREVSS lab test data used to be at T+4 weeks instead—but that seems to have changed to T+2 weeks now, as you note, evidently because (I will rashly conclude based on insufficient additional recent checking but lots of my research from 5 years ago,) the actually delays are almost all administrative, not technical! (Also, it’s super hard to do value of information in systems like this, as my dissertation concluded.)
This sounds like a really valuable project, and I’m glad you’re working on it! What sort of end-to-end latency (sample collection to analysis complete) do you think you might be able to achieve? For example, CDC Flu Virologic Surveillance has a latency of ~2 weeks (the most recent is currently from the week ending 2022-04-30, which I think means 12-18d since diagnosis), while MWRA Biobot typically posts data from two days ago each afternoon. If you’re trying to catch things with rapid growth, getting down to a day or lower is probably pretty important?
Yes—and since I did my dissertation partly to ask the question of how valuable it would be to reduce that delay, I feel compelled to note that the CDC’s syndromic surveillance data is at T+2 weeks, which isn’t actually based on diagnosis, but symptoms. The NREVSS lab test data used to be at T+4 weeks instead—but that seems to have changed to T+2 weeks now, as you note, evidently because (I will rashly conclude based on insufficient additional recent checking but lots of my research from 5 years ago,) the actually delays are almost all administrative, not technical! (Also, it’s super hard to do value of information in systems like this, as my dissertation concluded.)