Detecting Genetically Engineered Viruses With Metagenomic Sequencing

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.