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>eugenics but for chickens

So... animal husbandry?

The same for every species that has been domesticated. Corn, horses, dogs, even yeast.

This even happens to species we don’t intend to practice “eugenics” on. https://en.wikipedia.org/wiki/Vavilovian_mimicry

That'd be great if the viruses weren't also using accelerated evolution to become far more adept at infecting targets. By allowing the virus to spread unchecked, the chickens become a brilliant breeding ground for the virus and we're more likely to just breed stronger viruses (quite likely to be less virulent to chickens so that they can spread further, but also far more likely to jump between species).

Yes the idea is that birds that recover from bird flu will keep producing. You end up with more live birds than culling entire flocks. Some of the birds survive, because of their genetics.

You forgot about the part where the virus mutates and jumps to humans.

Too bad about the human race though, I guess.