Midwest Respiratory Virus Program (MRVP) Laboratory, Medical College of Wisconsin, Milwaukee, WI 53226, USA Department of Pediatric, Medical College of Wisconsin, Milwaukee, WI 53226, USA Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA Children’s Research Institute, Children’s Hospital of Wisconsin, P.O. Box 1997, Milwaukee, WI 53201-1997, USA Children’s Hospital of Wisconsin, P.O. Box 1997, Milwaukee, WI 53201-1997, USA Dynacare laboratories, Milwaukee, Wisconsin, USA Author to whom correspondence should be addressed. Abstract On 17 April 2009, novel swine origin influenza A virus (S-OIV) cases appeared within the United States. Most influenza A diagnostic assays currently utilized in local clinical laboratories do not allow definitive subtype determination. Detailed subtype analysis of influenza A positive samples in our laboratory allowed early confirmation of a large outbreak of S-OIV in southeastern Wisconsin (SEW). The initial case o