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I have some questions for you:
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I recently saw a patient who was positive for Lyme disease and he had a similar history of yelping randomly, but no other signs. I recommend having her tested. A simple blood test is involved, and if positive it is treatable with an antibiotic called doxycycline.
Other causes may include sore muscles from overexertion, a slipped disc in her back, and neck pain to list a few.
Your veterinarian will also be able to prescribe antiinflammatory and pain medications to keep her comfortable.
One last thought is separation anxiety:
Do any of those behaviors fit?