On-going unknown respiratory/fungal disease with chickens - several months - hoping for ID support

allvka_

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[PICTURES PROVIDED IN THREAD]
I have two chickens, one rooster and one hen. They both are free range. The rooster is around 1 and a half years old and my hen is 2 or 3 years old. They are both healthy weights.
Both birds have shown behaviors of shaking heads, itching ears, sneezing, and yawning. This has been going on for several months now, while trying to figure out what they are sick with.
My hen has stopped laying eggs completely.
About 3 or 4 months ago, my hen started showing pale discoloration on her comb/peak. It has gotten better while on voriconazole (antifungal) but has seemed to regress soon afterwards.
She has also started to have diarrhea.
My rooster, on the other hand, has normal poops.
My rooster has developed yellow fungal tips on his comb and has only gotten worse even while on antifungal.
He is losing feathers near the base of his comb.
There are no injuries.
I am unsure how this may have happened, it could have been environmental factors such as an unsanitary coop, toxins from an outside stream of water or contaminated controlled water source.
I have been cleaning the coop every weekend since they have gotten sick.
If anyone has any idea of what this may be and how to treat it, please tell me all you know. Thank you!
 
Here are pictures of both of my chickens.
 

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What is your general location in the world? Do you have any veterinarians where testing could be done? To me the lesions on the comb look like healing pecking injuries. They may appear black, then yellowish brown and later white. Have you checked the ears for any yellow discharge or checked the skin for mites or lice? There are a number of respiratory diseases including viruses or bacterial diseases. Infectious bronchitis virus can cause sneezing, congestion, head shaking, and may affect egg laying. It lasts about 3-4 weeks. Have you seen bubbles or foam in either of their eyes? Some hens may slow down laying after 3 years, or take breaks. If you are approaching winter, many hens stop laying until after the new year.
 

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