Hello, I'm Dr. Kara. I have over 20 years of experience as a veterinarian and I'd like to help with your concerns about Luke.
Even if his test for parvo-virus was negative it is still possible that he had that virus and it was early enough in the infection that his test wasn't positive yet. There are also countless other viruses and bacterial infections that can cause fever, vomiting, diarrhea and weakness that we don't vaccinate against that could have made him sick. We don't always know why our patients get sick, and it may be cost prohibitive to find out why so if they are improving we may not look any farther.
If he is feeling better, eating and drinking well again, then that is the important part. If he was quite dehydrated and was vomiting and having severe diarrhea it make take him several days to come along and get more active again.
If he isn't coming along and getting stronger in a few days perhaps we do need to look a closer for a reason behind his continued weakness. Congenital problems, such as a liver vessel abnormality called a portosystemic shunt or pancreatic insufficiency are other possible reasons for him to be sick.
If he hasn't been wormed and checked for gastrointestinal parasites those can also make small puppies very sick and those should be looked for.
I know that you are worried about him, and that is understandable because he is so little, but if he is steadily progressing he may just need more time.
Please let me know if you have any further questions.