Efficient Influenza A Virus Origin Detection

This research describes a novel, alignment-free method of genomic sequence comparisons based on absent nucleotide words and expression levels. Testing this method on Influenza A virus isolates, three classifications are presented which successfully identify; 1) the geographic origins of domestic bird H5N1 isolates through China and Southeast Asia during 2006, 2) the country of human H5N1 isolates crossing over from domestic bird hosts and, 3) the historical flu season from which human H3N2 isolates originated. Because comparison methods used do not rely on alignment, they are computationally efficient and well suited for large numbers of sequences in compehensive flu transmission network delineation.

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