Thank you for your question.
I am Dr. Su S. and I will try my best to help you.
There can be different causes for the chronic diarrhea.
Viral infection would not show up in routine stool test.
After an infection like viral there can be atrophy of villi causing malabsorption.
Malabsorption can come from other causes too.
Villi usually regenerates but may take time.
Depending on his age there can be inflammation.
As he is lethargic, I would advise to take him to ER.
There can be dehydration, electrolyte changes.
He can need IV fluid.
I hope this information will be helpful.
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Wish his healthy life.