Highly pathogenic avian influenza (HPAI) in poultry causes high morbidity and mortality, and it is a List A disease of the Office International des Epizooties. An outbreak of HPAI in commercial poultry not only causes direct disease losses but often results in trade restrictions for the affected country. Because HPAI viruses can mutate from H5 and H7 low pathogenic avian influenza viruses, it is necessary to monitor and control even the low pathogenic form of the virus.

We report a practical approach for screening large numbers of isolates that uses amplification by reverse transcriptase–polymerase chain reaction of a segment of the hemagglutinin (HA) gene (536–560 bp) of H7 avian influenza viruses followed by the heteroduplex mobility assay (HMA). The HMA test compares the amplified polymerase chain reaction product from unknown samples with reference isolates, which allows the identification of new variants. The HMA test results were compared with sequence analysis of the isolates used in the study. On the basis of the HMA, we could identify several new variant viruses present in the live bird markets in the northeastern United States. New strains gave a distinct pattern of bands in the gels in accordance with the different heteroduplexes formed when their HA region amplification products were incubated together with the same amplification product of a reference strain. These differences correlate with phylogenetic analysis from sequence data.