Genetic diversification of H5N1 highly pathogenic avian influenza A virus during replication in wild ducks

Highly pathogenic avian influenza A virus subtype H5N1 can potentially generate novel variants during replication of infected hosts. To determine which H5N1 variants predominate in wild birds, we determined the sequences of RT-PCR amplified viral genes from several organs of infected chickens and ducks from Egypt, where H5N1 outbreaks in birds are endemic. Comparison of the sequences in viruses from trachea, lung, brain and liver revealed diversification with different amino acid substitutions in different ducks, but no diversification in chickens. These specific amino acid substitutions were rare among viruses currently circulating in Egypt. In addition, the H5N1 variants showed distinct growth kinetics in duck, canine and human cells. Our findings suggested that ducks can generate H5N1 variants with novel amino acid substitutions that might serve as aetiological agents for new influenza virus outbreaks and epidemics.