Origins of the reassortant 2009 pandemic influenza virus through proteotyping with mass spectrometry

The application of a proteotyping approach employing high resolution mass spectrometry based is shown to be able to determine the gene origin of all major viral proteins in a triple reassortant pandemic 2009 influenza strain. Key to this approach is the identification of unique swine-host-specific signature and indicator peptides that are characteristic of influenza viruses circulating in North American and Eurasian swine herds in the years prior to the 2009 influenza pandemic. These swine-and human pandemic-specific signatures enable the origins of viral proteins in a clinical virus specimen to be determined and such strains to be rapidly and directly differentiated from other co-circulating seasonal influenza viruses from the same period. The proteotyping strategy offers advantages over traditional RT-PCR-based approaches that are currently the mainstay of influenza surveillance at the molecular level. Copyright (c) 2014 John Wiley & Sons, Ltd.