I think the point is that you have to sequence people in the hospital as well, otherwise you won't know if that particular strain is safe or not.

If it is a rare strain, how will you know if it's safe? Seems like it would have to be a rare strain with thousands of cases and hospitalizations in that population are extremely rare.

Sampling bias and other confounding factors would be a real problem in this search, at least from a statistical point of view, imo.

I also think finding everyone who has been infected with a strain isn't feasible, at best you are sampling from the population.