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With that history, the first thing that comes to mind is molluscum contagiosum. This is a viral infection which is fairly common in children and although it can be tenacious, most clear by a year or so. Minimizing contact with the lesions is key to limiting spread. In stubborn cases, medications such as cantharidin can be used, but should be avoided on the face due to a risk of scarring. Here's a link with more information: Molluscum Contagiosum
Let me know if the lesions pictured do not match the boy's lesions.