A method for detecting the emergence of potential pandemic-causing influenza strains has been developed. The system first uses real-time RT-PCR to detect H5, the highly pathogenic avian influenza subtype most likely to cause a pandemic. Pyrosequencing is then employed to scan for codon changes encoding amino acids known to define human influenza versus avian influenza signatures. The pyrosequencing assays were developed to screen at the nucleotide level for 52 amino acid changes defined as avian- or human-specific. A library has been built to screen the sequence data generated and properly identify the strain in question as a potential threat. This method can be used to screen samples for influenza and to determine if the detected virus contains mutations that may make the virus more infective or virulent to humans, potentially thwarting a pandemic outbreak.