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Are you still seeing fleas or flea dirt?
not really. but he is biting his paws and has an area on his chest that he is raw and starting to scab
A single flea bite can result in an itch for upto 6 weeks in dogs allergic to them. Oral Benadryl can be used at 1/2-1 mg per pound body weight every 8-12 hours as needed. If the itch persists there is something more going on, like seasonal allergies, and stronger meds from your vet will be needed. The raw areas should be cleaned twice a day with betadine or hydrogen peroxide, rinsed, dried and covered with Neosporin or bacitracin until they heal.
is there any kind of natural product I could wash him with, just for comfort,
The local pet store should have several anti-itch shampoos. Most are oatmeal based with an anti-histamine in them.