You can install screen on the vents to your coop as well as the chicken entrance. The screen will deter mosquitos, flies and gnats from getting inside the coop day or night. See pics below.
I've dealt with fowl pox. Depending on the severity of the strain, best case of it clearing up is about 4-6 weeks, worse case is a couple of months.
Once it passes through your flock, your birds will be immune to that particular strain thereafter. Eggs are safe to eat. Here's a couple of outside and inside pics with screen at the entrance. I used a razor blade to slice "strips" so that the chickens can pass through it.
All the vents are covered with hardware cloth and screen. All 3 of my coops have screen on the vents and at the entrance.
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