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virus or infection LONG

I have a sick horse that symptoms are really baffling me.  I wonder whether I could get a vet or two on the list to respond.  She seemed fine at home but when I got to a ride last weekend I first noticed she was reluctant to put her head down to graze.  I took her temp.  It was 102.  The ride vet examined  and found the rest of her vitals to be in normal range.  She was lethargic and I decide to take her home. No swelling anywhere.  By the morning her temp was 103.  I consulted a vet on the weekend and since she was eating and drinking the vet opted to put her on banamine and sulfamethoxazole/trimethoprim until the first of the week.  Her temp went as high as 104 before she would get her daily banamine. She went into the vet clinic on Monday. While on banamine she was acting quite normal. Temp 100.; some hoarse sound to her whinny, but acting quite like herself.
Blood work was done and the vet said she was raspy in the windpipe and some congestion in her lungs.  I am sure the vet believed that the horse would recover in the next day or so and that I was a little crazy when I said that she had some symptoms that the vet had not seen.  She was making strange mouth movements when eating and still had trouble putting her head to the ground.  ( kind of adjusted and rotated her head and not leaving it down long) Thinking back I now remembered that this head lowering problem had been coming on for a good week.  At water holes she would rush up and then not drink as usual, just rinse her mouth.  She also doesn't blow right, instead of the normal nose blow she does two less strong small nose blows. The blood work has come back with neutrophil seg 69 ; lymphocytes 21; monocytes 10; platelets adequate.  She has not been on banamine since Tuesday and her temp is running 100.8  She is now on antihistamine and doxycycline hyclate and is still having discomfit in her mouth it seems and does not like eating off the ground.  No nasal discharge only a SLIGHT nonproductive cough. Last night she was eating had this kind of choking problem and was backing up and making choking sounds before she relieved the blockage.   I have a two year old and a 12 year old who have not come down with any symptoms.  All horses are vaccinated yearly and have had nasal strangles vaccine.  I have attempted to look in her month for a problem and although this is just hold her tongue to the side with only a flashlight to see, we can't find anything.  She is scheduled to return to the vets on Monday for possible scoping and radiographs. But I can't help thinking something else is going on that we are missing.  If you have any advise or comments, I would like to hear them 

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