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My puppy has been scratching her neck area consistently since I got her. She is now 13 weeks old and it's too cold for fleas/ticks. The scratching continues. Today I noticed her skin is flakey there. Could this be an allergy?
 

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She is now 13 weeks old and it's too cold for fleas/ticks
no not the case especial tick and it is never too cold for fleas indoors but if the skin is flakey it could be Seborrhea which is a all to common inheritied skin condition in bassets. there is no cure but it can be controled with frequent ie 1 a week or more baths with an anti-seborrheic shampoo like selsun blue

Seborrhea
Primary seborrhea is most commonly seen in the American cocker spaniel, West Highland white terrier, English springer spaniel, and Basset hound. It is also seen in the Irish setter, German shepherd, dachshund, Doberman pinscher, Chinese Shar-pei, and Labrador retriever.

...Early evidence of the disorder such as mild flaking and dullness of the coat may appear as young as 10 weeks of age. Because these signs are subtle, they often go unnoticed. However, usually by a year to 18 months, the signs have become pronounced. Affected dogs commonly have a dull coat with excessive scaling, a greasy feel and smell to the skin (especially in areas of body folds), smelly waxy ears which may be infected, thickening of the foot pads, and dry brittle claws. Some breeds (West Highland white terrier, cocker spaniel, springer spaniel, Basset hound, Shar-pei) are more prone to the greasy form of seborrhea (seborrhea oleosa) with chronic ear infections and greasy skin,


seborrhea in dogs
Diet and Skin
Research has shown that dogs with seborrhea (oily, dandruffy skin) have depleted amounts of omega 6 fatty acids in their skin despite eating a diet that should be optimal. When omega 6 fatty acids are supplemented, the seborrhea improves. This finding supports the old time remedy of adding a spoonful of corn oil to the diet to ensure a glossy coat. It should be realized that seborrhea is complex condition but animals with seborrhea may need more omega 6 fatty acids.
Shampoo Therapy
 

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If I were you, I would wash the bedding frequently and make sure you rinse out all the soap really well because sometimes 'dust mites' can make them scratch, but of course it may not be what your pup has been troubled with, but old or unwashed bedding or chemicals in the soap powder not rinsed out, can make them itchy/scratchy.
 

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Possibly just dry skin. The heating systems in our homes dry out the skin much like our own be sure the food you feed is a good food and maybe putting a teaspoon of peanut oil on the food will help.
 

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it would be highly unusual for a dog 13 week or younger to show signs of actual allergic reaction. While susceptablity to developing allergies does appear to have some genetic component it take contact with allergens over time for allergies to develop usual 1-3 years.
 
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