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Sorry, I brain spasm-ed and wrote virus instead of bacteria :oops: . Apologies for any confusion. There are several strains though, so the rest still applies.

It's hard to predict. Different strains of the virus have different virulence. Stress of any kind can cause symptoms to flare. Any of the chronic diseases they can get can weaken the immune systems and allow other diseases to gain a foothold. It sounds like you are doing all you can to...

There are a lot of variables to your situation that we can't address. How much space between each coop and run for instance. How much biosecurity is really happening? The following article (not too long) I think addresses much of what you are asking. To vaccinate your birds you have to do...