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Hello,this is Dr. Jess. I am so sorry to hear about your puppies. Can you tell me if they had any vaccines yet, and how many they have already received? Has your vet looked at the stool for intestinal parasites such as coccidia and giardia in addition to worms?
It is possible that if they ran an in house parvo test, they could have had a false negative result. The test is pretty specific (a positive result is likely positive) but not always sensitive enough to pick up every case of parvo. Some of this can depending on the amount of sample, timing of sample, etc. You can read a little more about that here:http://www.aspcapro.org/resource/shelter-health-animal-care-disease-management/diagnosing-and-treating-parvovirus
Are they both on antivomiting medication, fluids, and antibiotics???